6JHG | pdb_00006jhg

Crystal structure of apo Pullulanase from Paenibacillus barengoltzii in space group P212121

PDB DOI: https://doi.org/10.2210/pdb6JHG/pdb
Entry: 6JHG supersedes: 5WWB

Classification: HYDROLASE
Organism(s): Paenibacillus barengoltzii
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-02-18 Released: 2019-03-06
Deposition Author(s): Wu, S.W., Yang, S.Q., Qin, Z., You, X., Huang, P., Jiang, Z.Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.201 (Depositor), 0.201 (DCC)
R-Value Work:
0.157 (Depositor), 0.158 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6JHG

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of apo Pullulanase from Paenibacillus barengoltzii in space group P212121

Wu, S.W., Yang, S.Q., Qin, Z., You, X., Huang, P., Jiang, Z.Q.

To be published.

Macromolecule Content

Total Structure Weight: 75.26 kDa
Atom Count: 5,878
Modeled Residue Count: 644
Deposited Residue Count: 675
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pulullanase	A	675	Paenibacillus barengoltzii	Mutation(s): 0 EC: 3.2.1.41
UniProt
Find proteins for A0A0C5GWS2 (Paenibacillus barengoltzii) Explore A0A0C5GWS2 Go to UniProtKB: A0A0C5GWS2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0C5GWS2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.201 (Depositor), 0.201 (DCC)
R-Value Work: 0.157 (Depositor), 0.158 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.457	α = 90
b = 78.834	β = 90
c = 116.038	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-03-06

Deposition Author(s):

This entry supersedes: 5WWB

Revision History (Full details and data files)

Version 1.0: 2019-03-06
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.