4LEF | pdb_00004lef

Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site

PDB DOI: https://doi.org/10.2210/pdb4LEF/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-25 Released: 2014-06-25
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed with phosphate in active site

Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 267.78 kDa
Atom Count: 20,380
Modeled Residue Count: 2,323
Deposited Residue Count: 2,336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase homology protein	A [auth C] B [auth D] C [auth A] D [auth B] E A [auth C], B [auth D], C [auth A], D [auth B], E, F, G, H	292	Escherichia coli K-12	Mutation(s): 0 Gene Names: php, yhfV, b3379, JW3342 EC: 3.1
UniProt
Find proteins for P45548 (Escherichia coli (strain K12)) Explore P45548 Go to UniProtKB: P45548
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45548
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain GA [auth B]	GA [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain GA [auth B] Interactions & Density Focus chain GA [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain YA [auth G] SDF format, chain Y [auth A] SDF format, chain XA [auth G] SDF format, chain X [auth A] SDF format, chain WA [auth G] SDF format, chain W [auth A] SDF format, chain VA [auth G] SDF format, chain V [auth A] SDF format, chain SA [auth F] SDF format, chain S [auth D] SDF format, chain RA [auth F] SDF format, chain R [auth D] SDF format, chain QA [auth F] SDF format, chain Q [auth D] SDF format, chain PA [auth F] SDF format, chain P [auth D] SDF format, chain MA [auth E] SDF format, chain M [auth C] SDF format, chain LA [auth E] SDF format, chain L [auth C] SDF format, chain KA [auth E] SDF format, chain K [auth C] SDF format, chain JA [auth E] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DB [auth H] SDF format, chain DA [auth B] SDF format, chain CB [auth H] SDF format, chain CA [auth B] SDF format, chain BB [auth H] SDF format, chain BA [auth B] MOL2 format, chain YA [auth G] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth G] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth G] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth G] MOL2 format, chain V [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth D] MOL2 format, chain RA [auth F] MOL2 format, chain R [auth D] MOL2 format, chain QA [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain PA [auth F] MOL2 format, chain P [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain M [auth C] MOL2 format, chain LA [auth E] MOL2 format, chain L [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain K [auth C] MOL2 format, chain JA [auth E] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DB [auth H] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth H] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth H] MOL2 format, chain BA [auth B] mmCIF format, chain YA [auth G] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth G] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth G] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth G] mmCIF format, chain V [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth D] mmCIF format, chain RA [auth F] mmCIF format, chain R [auth D] mmCIF format, chain QA [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain PA [auth F] mmCIF format, chain P [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain M [auth C] mmCIF format, chain LA [auth E] mmCIF format, chain L [auth C] mmCIF format, chain KA [auth E] mmCIF format, chain K [auth C] mmCIF format, chain JA [auth E] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DB [auth H] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth H] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth H] mmCIF format, chain BA [auth B]	BA [auth B] BB [auth H] CA [auth B] CB [auth H] DA [auth B] BA [auth B], BB [auth H], CA [auth B], CB [auth H], DA [auth B], DB [auth H], EA [auth B], FA [auth B], JA [auth E], K [auth C], KA [auth E], L [auth C], LA [auth E], M [auth C], MA [auth E], P [auth D], PA [auth F], Q [auth D], QA [auth F], R [auth D], RA [auth F], S [auth D], SA [auth F], V [auth A], VA [auth G], W [auth A], WA [auth G], X [auth A], XA [auth G], Y [auth A], YA [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth B] Focus chain BB [auth H] Focus chain CA [auth B] Focus chain CB [auth H] Focus chain DA [auth B] Focus chain DB [auth H] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain JA [auth E] Focus chain K [auth C] Focus chain KA [auth E] Focus chain L [auth C] Focus chain LA [auth E] Focus chain M [auth C] Focus chain MA [auth E] Focus chain P [auth D] Focus chain PA [auth F] Focus chain Q [auth D] Focus chain QA [auth F] Focus chain R [auth D] Focus chain RA [auth F] Focus chain S [auth D] Focus chain SA [auth F] Focus chain V [auth A] Focus chain VA [auth G] Focus chain W [auth A] Focus chain WA [auth G] Focus chain X [auth A] Focus chain XA [auth G] Focus chain Y [auth A] Focus chain YA [auth G] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth H] Focus chain CA [auth B] Focus chain CB [auth H] Focus chain DA [auth B] Focus chain DB [auth H] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain JA [auth E] Focus chain K [auth C] Focus chain KA [auth E] Focus chain L [auth C] Focus chain LA [auth E] Focus chain M [auth C] Focus chain MA [auth E] Focus chain P [auth D] Focus chain PA [auth F] Focus chain Q [auth D] Focus chain QA [auth F] Focus chain R [auth D] Focus chain RA [auth F] Focus chain S [auth D] Focus chain SA [auth F] Focus chain V [auth A] Focus chain VA [auth G] Focus chain W [auth A] Focus chain WA [auth G] Focus chain X [auth A] Focus chain XA [auth G] Focus chain Y [auth A] Focus chain YA [auth G]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain Z [auth B] SDF format, chain UA [auth G] SDF format, chain U [auth A] SDF format, chain TA [auth G] SDF format, chain T [auth A] SDF format, chain OA [auth F] SDF format, chain O [auth D] SDF format, chain NA [auth F] SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain IA [auth E] SDF format, chain I [auth C] SDF format, chain HA [auth E] SDF format, chain AB [auth H] SDF format, chain AA [auth B] MOL2 format, chain ZA [auth H] MOL2 format, chain Z [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth G] MOL2 format, chain T [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain O [auth D] MOL2 format, chain NA [auth F] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain IA [auth E] MOL2 format, chain I [auth C] MOL2 format, chain HA [auth E] MOL2 format, chain AB [auth H] MOL2 format, chain AA [auth B] mmCIF format, chain ZA [auth H] mmCIF format, chain Z [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth G] mmCIF format, chain T [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain O [auth D] mmCIF format, chain NA [auth F] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain IA [auth E] mmCIF format, chain I [auth C] mmCIF format, chain HA [auth E] mmCIF format, chain AB [auth H] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth H] HA [auth E] I [auth C] IA [auth E] AA [auth B], AB [auth H], HA [auth E], I [auth C], IA [auth E], J [auth C], N [auth D], NA [auth F], O [auth D], OA [auth F], T [auth A], TA [auth G], U [auth A], UA [auth G], Z [auth B], ZA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth H] Focus chain HA [auth E] Focus chain I [auth C] Focus chain IA [auth E] Focus chain J [auth C] Focus chain N [auth D] Focus chain NA [auth F] Focus chain O [auth D] Focus chain OA [auth F] Focus chain T [auth A] Focus chain TA [auth G] Focus chain U [auth A] Focus chain UA [auth G] Focus chain Z [auth B] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth H] Focus chain HA [auth E] Focus chain I [auth C] Focus chain IA [auth E] Focus chain J [auth C] Focus chain N [auth D] Focus chain NA [auth F] Focus chain O [auth D] Focus chain OA [auth F] Focus chain T [auth A] Focus chain TA [auth G] Focus chain U [auth A] Focus chain UA [auth G] Focus chain Z [auth B] Focus chain ZA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.208 (Depositor), 0.208 (DCC)
R-Value Work: 0.175 (Depositor), 0.175 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.048	α = 90
b = 100.308	β = 104.48
c = 168.037	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-06-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-06-25
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary