[English] 日本語
Yorodumi
- PDB-3m1r: The crystal structure of formimidoylglutamase from Bacillus subti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m1r
TitleThe crystal structure of formimidoylglutamase from Bacillus subtilis subsp. subtilis str. 168
ComponentsFormimidoylglutamase
KeywordsHYDROLASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Histidine metabolism / Manganese / Metal-binding
Function / homology
Function and homology information


formimidoylglutamase / formimidoylglutamase activity / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / manganese ion binding
Similarity search - Function
Formiminoglutamase / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / DI(HYDROXYETHYL)ETHER / Formimidoylglutamase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.199 Å
AuthorsTan, K. / Bigelow, L. / Trevino, D. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of formimidoylglutamase from Bacillus subtilis subsp. subtilis str. 168
Authors: Tan, K. / Bigelow, L. / Buck, K. / Joachimiak, A.
History
DepositionMar 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formimidoylglutamase
B: Formimidoylglutamase
C: Formimidoylglutamase
D: Formimidoylglutamase
E: Formimidoylglutamase
F: Formimidoylglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,05252
Polymers214,5376
Non-polymers3,51546
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36870 Å2
ΔGint-287 kcal/mol
Surface area59310 Å2
MethodPISA
2
A: Formimidoylglutamase
B: Formimidoylglutamase
C: Formimidoylglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,13228
Polymers107,2693
Non-polymers1,86425
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-101 kcal/mol
Surface area35530 Å2
MethodPISA
3
D: Formimidoylglutamase
E: Formimidoylglutamase
F: Formimidoylglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,92024
Polymers107,2693
Non-polymers1,65121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-97 kcal/mol
Surface area35840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.038, 118.980, 123.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Formimidoylglutamase / / Formiminoglutamase / Formiminoglutamate hydrolase


Mass: 35756.176 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: str. 168 / Gene: hutG, BSU39380, EE57C / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: P42068, formimidoylglutamase

-
Non-polymers , 5 types, 299 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MgCl2, 0.1M Sodium cacodylate, 50% (v/v) PEG200, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 19, 2009 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.25→32.5 Å / Num. all: 102844 / Num. obs: 102844 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 30.6
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5103 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.199→32.474 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 4749 5.06 %random
Rwork0.1764 ---
all0.1791 93772 --
obs0.1791 93772 88.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.229 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.8931 Å20 Å20 Å2
2--6.3292 Å2-0 Å2
3---3.564 Å2
Refinement stepCycle: LAST / Resolution: 2.199→32.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14716 0 202 253 15171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815195
X-RAY DIFFRACTIONf_angle_d1.15420558
X-RAY DIFFRACTIONf_dihedral_angle_d19.3425538
X-RAY DIFFRACTIONf_chiral_restr0.0742331
X-RAY DIFFRACTIONf_plane_restr0.0052650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1991-2.27770.29723160.21645487X-RAY DIFFRACTION55
2.2777-2.36890.26114370.19698369X-RAY DIFFRACTION83
2.3689-2.47660.28524660.19478465X-RAY DIFFRACTION85
2.4766-2.60710.24584870.18238829X-RAY DIFFRACTION88
2.6071-2.77040.27984550.19559026X-RAY DIFFRACTION90
2.7704-2.98420.25975030.19839169X-RAY DIFFRACTION91
2.9842-3.28420.27195000.19559595X-RAY DIFFRACTION95
3.2842-3.75890.2285000.17049866X-RAY DIFFRACTION97
3.7589-4.73340.17915330.139710017X-RAY DIFFRACTION98
4.7334-32.47750.20695520.167410200X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.88240.55540.10090.47220.1991.27050.2436-0.0432-0.69780.1669-0.1029-0.53210.2179-0.0027-0.15990.2039-0.0266-0.17260.09560.04770.531425.742751.259812.9868
21.66230.84230.46441.03970.04550.82630.1149-0.80780.32820.1295-0.2450.09140.0261-0.48760.14570.2273-0.06830.02470.5963-0.17250.1993-5.508671.300623.3667
31.53780.40610.5931.0258-0.03811.2093-0.13950.10920.069-0.03280.04380.0081-0.31940.18440.09710.2706-0.0794-0.05110.13490.03060.247618.171784.5333-3.9422
42.14320.2645-0.45910.82570.48381.208-0.1066-0.0587-0.71730.04560.02280.0630.2866-0.09740.07760.2044-0.05250.03590.11420.03820.4145-10.784435.0168-0.0107
51.5360.1293-0.260.7754-0.16951.25860.15080.44580.03740.0039-0.06910.1566-0.1127-0.4319-0.10030.19910.1112-0.00090.36630.05350.2-21.529368.6164-15.0863
61.8011-0.1896-0.1431.52880.06310.9895-0.06010.5361-0.1765-0.150.0356-0.3157-0.0302-0.12050.00140.1423-0.04290.09840.2849-0.12650.200810.122151.2651-28.3538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-1 - 318
2X-RAY DIFFRACTION2chain BB1 - 317
3X-RAY DIFFRACTION3chain CC2 - 317
4X-RAY DIFFRACTION4chain DD-2 - 318
5X-RAY DIFFRACTION5chain EE2 - 317
6X-RAY DIFFRACTION6chain FF3 - 318

+
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