2YBD | pdb_00002ybd

Crystal structure of probable had family hydrolase from pseudomonas fluorescens pf-5 with bound phosphate

PDB DOI: https://doi.org/10.2210/pdb2YBD/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas protegens Pf-5
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-03 Released: 2011-03-16
Deposition Author(s): Vetting, M.W., Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.218 (Depositor), 0.208 (DCC)
R-Value Work:
0.171 (Depositor), 0.162 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of Probable Had Family Hydrolase from Pseudomonas Fluorescens Pf-5 with Bound Phosphate

Vetting, M.W., Patskovsky, Y., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 22.98 kDa
Atom Count: 1,782
Modeled Residue Count: 196
Deposited Residue Count: 205
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY	A	205	Pseudomonas protegens Pf-5	Mutation(s): 0
UniProt
Find proteins for Q4K5L5 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K5L5 Go to UniProtKB: Q4K5L5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4K5L5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	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: 0.218 (Depositor), 0.208 (DCC)
R-Value Work: 0.171 (Depositor), 0.162 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.978	α = 90
b = 65.978	β = 90
c = 250.4	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-16
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-07-05
Changes: Data collection
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Other, Structure summary
Version 1.5: 2023-12-20
Changes: Data collection, Database references, Refinement description
Version 1.6: 2024-11-13
Changes: Structure summary