3NRJ | pdb_00003nrj

Crystal structure of probable yrbi family phosphatase from pseudomonas syringae pv.phaseolica 1448a complexed with magnesium

PDB DOI: https://doi.org/10.2210/pdb3NRJ/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas savastanoi pv. phaseolicola 1448A
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-06-30 Released: 2010-07-28
Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Freeman, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.240 (Depositor), 0.239 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Had Family Hydrolase from Pseudomonas Syringae Pv.Phaseolica 1448A

Patskovsky, Y., Ramagopal, U., Toro, R., Freeman, J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 249.98 kDa
Atom Count: 17,050
Modeled Residue Count: 2,081
Deposited Residue Count: 2,268
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE YRBI FAMILY PHOSPHATASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	189	Pseudomonas savastanoi pv. phaseolicola 1448A	Mutation(s): 1 Gene Names: PSPPH_4147 EC: 3.1.3.45
UniProt
Find proteins for Q48EB9 (Pseudomonas savastanoi pv. phaseolicola (strain 1448A / Race 6)) Explore Q48EB9 Go to UniProtKB: Q48EB9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q48EB9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain XA [auth L] SDF format, chain W [auth C] SDF format, chain UA [auth K] SDF format, chain T [auth B] SDF format, chain RA [auth J] SDF format, chain P [auth A] SDF format, chain OA [auth I] SDF format, chain MA [auth H] SDF format, chain KA [auth G] SDF format, chain FA [auth F] SDF format, chain CA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain XA [auth L] MOL2 format, chain W [auth C] MOL2 format, chain UA [auth K] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth J] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth I] MOL2 format, chain MA [auth H] MOL2 format, chain KA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain XA [auth L] mmCIF format, chain W [auth C] mmCIF format, chain UA [auth K] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth J] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth I] mmCIF format, chain MA [auth H] mmCIF format, chain KA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] FA [auth F] KA [auth G] MA [auth H] OA [auth I] CA [auth E], FA [auth F], KA [auth G], MA [auth H], OA [auth I], P [auth A], RA [auth J], T [auth B], UA [auth K], W [auth C], XA [auth L], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain OA [auth I] Focus chain P [auth A] Focus chain RA [auth J] Focus chain T [auth B] Focus chain UA [auth K] Focus chain W [auth C] Focus chain XA [auth L] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain OA [auth I] Focus chain P [auth A] Focus chain RA [auth J] Focus chain T [auth B] Focus chain UA [auth K] Focus chain W [auth C] Focus chain XA [auth L] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain VA [auth L] SDF format, chain U [auth C] SDF format, chain SA [auth K] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain IA [auth G] SDF format, chain HA [auth G] SDF format, chain GA [auth F] SDF format, chain DA [auth F] SDF format, chain AA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain VA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain SA [auth K] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain VA [auth L] mmCIF format, chain U [auth C] mmCIF format, chain SA [auth K] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] DA [auth F] GA [auth F] HA [auth G] IA [auth G] AA [auth E], DA [auth F], GA [auth F], HA [auth G], IA [auth G], M [auth A], N [auth A], Q [auth B], R [auth B], SA [auth K], U [auth C], VA [auth L], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain WA [auth L] SDF format, chain V [auth C] SDF format, chain TA [auth K] SDF format, chain S [auth B] SDF format, chain QA [auth J] SDF format, chain O [auth A] SDF format, chain NA [auth I] SDF format, chain LA [auth H] SDF format, chain JA [auth G] SDF format, chain EA [auth F] SDF format, chain BA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain WA [auth L] MOL2 format, chain V [auth C] MOL2 format, chain TA [auth K] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain LA [auth H] MOL2 format, chain JA [auth G] MOL2 format, chain EA [auth F] MOL2 format, chain BA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain WA [auth L] mmCIF format, chain V [auth C] mmCIF format, chain TA [auth K] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth J] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain LA [auth H] mmCIF format, chain JA [auth G] mmCIF format, chain EA [auth F] mmCIF format, chain BA [auth E]	BA [auth E] EA [auth F] JA [auth G] LA [auth H] NA [auth I] BA [auth E], EA [auth F], JA [auth G], LA [auth H], NA [auth I], O [auth A], QA [auth J], S [auth B], TA [auth K], V [auth C], WA [auth L], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain NA [auth I] Focus chain O [auth A] Focus chain QA [auth J] Focus chain S [auth B] Focus chain TA [auth K] Focus chain V [auth C] Focus chain WA [auth L] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain NA [auth I] Focus chain O [auth A] Focus chain QA [auth J] Focus chain S [auth B] Focus chain TA [auth K] Focus chain V [auth C] Focus chain WA [auth L] Focus chain Y [auth D]
UNL Query on UNL Download:Ideal Coordinates CCD File	PA [auth I]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain PA [auth I] Interactions & Density Focus chain PA [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240 (Depositor), 0.239 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.302	α = 90
b = 126.733	β = 95.57
c = 106.531	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-07-28

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2021-10-06
Changes: Database references
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description