2PNK | pdb_00002pnk

CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2PNK/pdb

Classification: ISOMERASE
Organism(s): Halalkalibacterium halodurans C-125
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-24 Released: 2007-05-08
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.178 (Depositor), 0.232 (DCC)
R-Value Work:
0.148 (Depositor), 0.156 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.8 of the entry. See complete history.

Literature

Crystal structure of uncharacterized protein (NP_241359.1) from Bacillus halodurans at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 614.81 kDa
Atom Count: 45,764
Modeled Residue Count: 5,042
Deposited Residue Count: 5,136
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH0493 protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	428	Halalkalibacterium halodurans C-125	Mutation(s): 17 Gene Names: NP_241359.1, BH0493
UniProt
Find proteins for Q9KFI6 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KFI6 Go to UniProtKB: Q9KFI6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KFI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain YB [auth L] SDF format, chain Y [auth C] SDF format, chain SB [auth K] SDF format, chain RB [auth K] SDF format, chain RA [auth G] SDF format, chain QA [auth G] MOL2 format, chain YB [auth L] MOL2 format, chain Y [auth C] MOL2 format, chain SB [auth K] MOL2 format, chain RB [auth K] MOL2 format, chain RA [auth G] MOL2 format, chain QA [auth G] mmCIF format, chain YB [auth L] mmCIF format, chain Y [auth C] mmCIF format, chain SB [auth K] mmCIF format, chain RB [auth K] mmCIF format, chain RA [auth G] mmCIF format, chain QA [auth G]	QA [auth G] RA [auth G] RB [auth K] SB [auth K] Y [auth C] QA [auth G], RA [auth G], RB [auth K], SB [auth K], Y [auth C], YB [auth L]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain QA [auth G] Focus chain RA [auth G] Focus chain RB [auth K] Focus chain SB [auth K] Focus chain Y [auth C] Focus chain YB [auth L] Interactions & Density Focus chain QA [auth G] Focus chain RA [auth G] Focus chain RB [auth K] Focus chain SB [auth K] Focus chain Y [auth C] Focus chain YB [auth L]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain LB [auth K] SDF format, chain IA [auth F] SDF format, chain AA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain LB [auth K] MOL2 format, chain IA [auth F] MOL2 format, chain AA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain LB [auth K] mmCIF format, chain IA [auth F] mmCIF format, chain AA [auth D]	AA [auth D], IA [auth F], LB [auth K], W [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth D] Focus chain IA [auth F] Focus chain LB [auth K] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain IA [auth F] Focus chain LB [auth K] Focus chain W [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain YA [auth H] SDF format, chain XB [auth L] SDF format, chain XA [auth H] SDF format, chain WB [auth L] SDF format, chain WA [auth H] SDF format, chain V [auth B] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain QB [auth K] SDF format, chain Q [auth A] SDF format, chain PB [auth K] SDF format, chain PA [auth G] SDF format, chain P [auth A] SDF format, chain OB [auth K] SDF format, chain NB [auth K] SDF format, chain KB [auth J] SDF format, chain JB [auth J] SDF format, chain HA [auth E] SDF format, chain GA [auth E] SDF format, chain EA [auth D] SDF format, chain DB [auth I] SDF format, chain DA [auth D] SDF format, chain CB [auth I] MOL2 format, chain ZA [auth H] MOL2 format, chain YA [auth H] MOL2 format, chain XB [auth L] MOL2 format, chain XA [auth H] MOL2 format, chain WB [auth L] MOL2 format, chain WA [auth H] MOL2 format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain QB [auth K] MOL2 format, chain Q [auth A] MOL2 format, chain PB [auth K] MOL2 format, chain PA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth K] MOL2 format, chain NB [auth K] MOL2 format, chain KB [auth J] MOL2 format, chain JB [auth J] MOL2 format, chain HA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth I] MOL2 format, chain DA [auth D] MOL2 format, chain CB [auth I] mmCIF format, chain ZA [auth H] mmCIF format, chain YA [auth H] mmCIF format, chain XB [auth L] mmCIF format, chain XA [auth H] mmCIF format, chain WB [auth L] mmCIF format, chain WA [auth H] mmCIF format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain QB [auth K] mmCIF format, chain Q [auth A] mmCIF format, chain PB [auth K] mmCIF format, chain PA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth K] mmCIF format, chain NB [auth K] mmCIF format, chain KB [auth J] mmCIF format, chain JB [auth J] mmCIF format, chain HA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth I] mmCIF format, chain DA [auth D] mmCIF format, chain CB [auth I]	CB [auth I] DA [auth D] DB [auth I] EA [auth D] GA [auth E] CB [auth I], DA [auth D], DB [auth I], EA [auth D], GA [auth E], HA [auth E], JB [auth J], KB [auth J], NB [auth K], OB [auth K], P [auth A], PA [auth G], PB [auth K], Q [auth A], QB [auth K], R [auth A], S [auth A], V [auth B], WA [auth H], WB [auth L], XA [auth H], XB [auth L], YA [auth H], ZA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain JB [auth J] Focus chain KB [auth J] Focus chain NB [auth K] Focus chain OB [auth K] Focus chain P [auth A] Focus chain PA [auth G] Focus chain PB [auth K] Focus chain Q [auth A] Focus chain QB [auth K] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain WA [auth H] Focus chain WB [auth L] Focus chain XA [auth H] Focus chain XB [auth L] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain JB [auth J] Focus chain KB [auth J] Focus chain NB [auth K] Focus chain OB [auth K] Focus chain P [auth A] Focus chain PA [auth G] Focus chain PB [auth K] Focus chain Q [auth A] Focus chain QB [auth K] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain WA [auth H] Focus chain WB [auth L] Focus chain XA [auth H] Focus chain XB [auth L] Focus chain YA [auth H] Focus chain ZA [auth H]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain UB [auth L] SDF format, chain JA [auth F] SDF format, chain AB [auth I] MOL2 format, chain UB [auth L] MOL2 format, chain JA [auth F] MOL2 format, chain AB [auth I] mmCIF format, chain UB [auth L] mmCIF format, chain JA [auth F] mmCIF format, chain AB [auth I]	AB [auth I], JA [auth F], UB [auth L]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AB [auth I] Focus chain JA [auth F] Focus chain UB [auth L] Interactions & Density Focus chain AB [auth I] Focus chain JA [auth F] Focus chain UB [auth L]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain VB [auth L] SDF format, chain VA [auth H] SDF format, chain U [auth B] SDF format, chain OA [auth G] SDF format, chain O [auth A] SDF format, chain MB [auth K] SDF format, chain KA [auth F] SDF format, chain IB [auth J] SDF format, chain HB [auth J] SDF format, chain FA [auth E] SDF format, chain CA [auth D] SDF format, chain BB [auth I] SDF format, chain BA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain VB [auth L] MOL2 format, chain VA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain MB [auth K] MOL2 format, chain KA [auth F] MOL2 format, chain IB [auth J] MOL2 format, chain HB [auth J] MOL2 format, chain FA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain BA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain VB [auth L] mmCIF format, chain VA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain MB [auth K] mmCIF format, chain KA [auth F] mmCIF format, chain IB [auth J] mmCIF format, chain HB [auth J] mmCIF format, chain FA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain BA [auth D]	BA [auth D] BB [auth I] CA [auth D] FA [auth E] HB [auth J] BA [auth D], BB [auth I], CA [auth D], FA [auth E], HB [auth J], IB [auth J], KA [auth F], MB [auth K], O [auth A], OA [auth G], U [auth B], VA [auth H], VB [auth L], X [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain FA [auth E] Focus chain HB [auth J] Focus chain IB [auth J] Focus chain KA [auth F] Focus chain MB [auth K] Focus chain O [auth A] Focus chain OA [auth G] Focus chain U [auth B] Focus chain VA [auth H] Focus chain VB [auth L] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain FA [auth E] Focus chain HB [auth J] Focus chain IB [auth J] Focus chain KA [auth F] Focus chain MB [auth K] Focus chain O [auth A] Focus chain OA [auth G] Focus chain U [auth B] Focus chain VA [auth H] Focus chain VB [auth L] Focus chain X [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain TB [auth L] SDF format, chain TA [auth H] SDF format, chain NA [auth G] SDF format, chain N [auth A] SDF format, chain MA [auth G] SDF format, chain LA [auth G] SDF format, chain FB [auth J] MOL2 format, chain Z [auth D] MOL2 format, chain TB [auth L] MOL2 format, chain TA [auth H] MOL2 format, chain NA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain FB [auth J] mmCIF format, chain Z [auth D] mmCIF format, chain TB [auth L] mmCIF format, chain TA [auth H] mmCIF format, chain NA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain FB [auth J]	FB [auth J] LA [auth G] MA [auth G] N [auth A] NA [auth G] FB [auth J], LA [auth G], MA [auth G], N [auth A], NA [auth G], TA [auth H], TB [auth L], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FB [auth J] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain TA [auth H] Focus chain TB [auth L] Focus chain Z [auth D] Interactions & Density Focus chain FB [auth J] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain TA [auth H] Focus chain TB [auth L] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain SA [auth H] SDF format, chain M [auth A] SDF format, chain EB [auth J] MOL2 format, chain SA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain EB [auth J] mmCIF format, chain SA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain EB [auth J]	EB [auth J], M [auth A], SA [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EB [auth J] Focus chain M [auth A] Focus chain SA [auth H] Interactions & Density Focus chain EB [auth J] Focus chain M [auth A] Focus chain SA [auth H]
UNL Query on UNL Download:Ideal Coordinates CCD File	GB [auth J], T [auth B], UA [auth H]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain GB [auth J] Focus chain T [auth B] Focus chain UA [auth H] Interactions & Density Focus chain GB [auth J] Focus chain T [auth B] Focus chain UA [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.178 (Depositor), 0.232 (DCC)
R-Value Work: 0.148 (Depositor), 0.156 (DCC)
R-Value Observed: 0.149 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 273.72	α = 90
b = 158.56	β = 116.03
c = 181.24	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
MOLREP	phasing
SHELXD	phasing
autoSHARP	phasing