[English] 日本語
Yorodumi
- PDB-4gyr: Granulibacter bethesdensis allophanate hydrolase apo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gyr
TitleGranulibacter bethesdensis allophanate hydrolase apo
ComponentsAllophanate hydrolase
KeywordsHYDROLASE / Amidase signature family enzyme
Function / homology
Function and homology information


allophanate hydrolase / allophanate hydrolase activity
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1700 / Allophanate hydrolase / : / Allophanate hydrolase C-terminal domain / Amidase / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1700 / Allophanate hydrolase / : / Allophanate hydrolase C-terminal domain / Amidase / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Allophanate hydrolase
Similarity search - Component
Biological speciesGranulibacter bethesdensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLin, Y. / St Maurice, M.
CitationJournal: Biochemistry / Year: 2013
Title: The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family.
Authors: Lin, Y. / St Maurice, M.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Allophanate hydrolase
B: Allophanate hydrolase


Theoretical massNumber of molelcules
Total (without water)133,0742
Polymers133,0742
Non-polymers00
Water2,090116
1
B: Allophanate hydrolase

A: Allophanate hydrolase


Theoretical massNumber of molelcules
Total (without water)133,0742
Polymers133,0742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x-y,x+1,z+1/61
2
A: Allophanate hydrolase


Theoretical massNumber of molelcules
Total (without water)66,5371
Polymers66,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Allophanate hydrolase


Theoretical massNumber of molelcules
Total (without water)66,5371
Polymers66,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.094, 78.094, 397.543
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:46 or resseq 48:346 or resseq 348:462 )
211chain B and (resseq 2:46 or resseq 48:346 or resseq 348:462 )
DetailsThe biological unit consists of chain A from Sym ID 6_565 and chain B from the identity matrix (Sym ID 1_555)

-
Components

#1: Protein Allophanate hydrolase


Mass: 66537.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Granulibacter bethesdensis (bacteria) / Strain: ATCC BAA-1260 / CGDNIH1 / Gene: GbCGDNIH1_1744 / Plasmid: pET28a-(HIS)8-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q0BRB0, allophanate hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24%(w/v)PEG4000,50mM MgCl2,100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 33600 / Num. obs: 33519 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 20.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 18.1 / Num. unique all: 1634 / % possible all: 100

-
Processing

Software
NameVersionClassification
MC-2diffractometer software from EMBLdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GYS

4gys


Resolution: 2.8→40.045 Å / SU ML: 0.88 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3068 2026 6.05 %RANDOM
Rwork0.2562 ---
obs0.2594 33489 99.87 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.529 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.9635 Å2-0 Å2-0 Å2
2--4.9635 Å20 Å2
3----9.2344 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6806 0 0 116 6922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056958
X-RAY DIFFRACTIONf_angle_d0.9069507
X-RAY DIFFRACTIONf_dihedral_angle_d17.3862473
X-RAY DIFFRACTIONf_chiral_restr0.0591107
X-RAY DIFFRACTIONf_plane_restr0.0041258
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3370X-RAY DIFFRACTIONPOSITIONAL
12B3370X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.87030.36261450.29642234X-RAY DIFFRACTION100
2.8703-2.94780.35641450.2992233X-RAY DIFFRACTION100
2.9478-3.03460.35231440.28322251X-RAY DIFFRACTION100
3.0346-3.13250.37421430.28562274X-RAY DIFFRACTION100
3.1325-3.24440.34571430.28222237X-RAY DIFFRACTION100
3.2444-3.37420.33051480.2672246X-RAY DIFFRACTION100
3.3742-3.52770.31051450.27722231X-RAY DIFFRACTION100
3.5277-3.71360.35611470.25962267X-RAY DIFFRACTION100
3.7136-3.9460.31481380.2432232X-RAY DIFFRACTION100
3.946-4.25040.29451510.22642244X-RAY DIFFRACTION100
4.2504-4.67760.24971450.21312247X-RAY DIFFRACTION100
4.6776-5.3530.29071420.22452252X-RAY DIFFRACTION100
5.353-6.73910.30441440.27832252X-RAY DIFFRACTION100
6.7391-40.04940.24021460.25862263X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more