8H7P | pdb_00008h7p

Crystal structure of aqualigase bound with Suc-AAPF

PDB DOI: https://doi.org/10.2210/pdb8H7P/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis, synthetic construct
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2022-10-20 Released: 2023-11-01
Deposition Author(s): Li, H., Ma, M.Z., Zhang, L.J., Dai, L., Chen, C.-C., Guo, R.-T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.189 (Depositor), 0.198 (DCC)
R-Value Work:
0.135 (Depositor), 0.147 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8H7P

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

Literature

Crystal structure of aqualigase bound with Suc-AAPF

Li, H., Ma, M.Z., Zhang, L.J., Dai, L., Chen, C.-C., Guo, R.-T.

To be published.

Macromolecule Content

Total Structure Weight: 29.06 kDa
Atom Count: 2,268
Modeled Residue Count: 287
Deposited Residue Count: 287
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin	A	281	Bacillus subtilis	Mutation(s): 0 Gene Names: KS08_04965 EC: 3.4.21.62

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE	B	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.189 (Depositor), 0.198 (DCC)
R-Value Work: 0.135 (Depositor), 0.147 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.578	α = 90
b = 71.68	β = 114.74
c = 40.804	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data scaling
PDB_EXTRACT	data extraction
SAINT	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-11-01
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.