[English] 日本語
Yorodumi
- PDB-3orr: Crystal Structure of N5-Carboxyaminoimidazole synthetase from Sta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3orr
TitleCrystal Structure of N5-Carboxyaminoimidazole synthetase from Staphylococcus aureus
ComponentsN5-carboxyaminoimidazole ribonucleotide synthetase
KeywordsLIGASE / BIOSYNTHETIC PROTEIN / ATP-grasp superfamily
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / NAD binding / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N5-carboxyaminoimidazole ribonucleotide synthase / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.23 Å
AuthorsBrugarolas, P. / Duguid, E.M. / Zhang, W. / Poor, C.B. / He, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus.
Authors: Brugarolas, P. / Duguid, E.M. / Zhang, W. / Poor, C.B. / He, C.
History
DepositionSep 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 24, 2013Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N5-carboxyaminoimidazole ribonucleotide synthetase
B: N5-carboxyaminoimidazole ribonucleotide synthetase


Theoretical massNumber of molelcules
Total (without water)86,4772
Polymers86,4772
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-12 kcal/mol
Surface area29620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.112, 53.327, 107.406
Angle α, β, γ (deg.)90.00, 95.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein N5-carboxyaminoimidazole ribonucleotide synthetase / Phosphoribosylaminoimidazole carboxylase / ATPase subunit


Mass: 43238.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Newman / Gene: NWMN_0934, purK / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star
References: UniProt: A6QFS4, UniProt: A0A0H3KFM7*PLUS, 5-(carboxyamino)imidazole ribonucleotide synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.1 M BIS-TRIS, 28% w/v polyethylene glycol monomethyl ether 2,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951, 0.97937, 0.97196
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979511
20.979371
30.971961
ReflectionResolution: 2.23→50 Å / Num. obs: 34628 / % possible obs: 83.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 %
Reflection shellResolution: 2.23→2.4 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.64 / Rsym value: 0.46 / % possible all: 45.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.23→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.489 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1869 5.1 %RANDOM
Rwork0.194 ---
obs0.197 34554 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å2-0.61 Å2
2--2.29 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.23→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5881 0 0 215 6096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9568087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54725.973298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.118151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2191518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2899
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0121.53658
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9425925
X-RAY DIFFRACTIONr_scbond_it2.76332338
X-RAY DIFFRACTIONr_scangle_it4.5014.52162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 150 -
Rwork0.256 2468 -
obs--98.72 %
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)
10.20840.09280.1260.60210.15450.6082-0.01830.06070.1373-0.0167-0.056-0.00850.03810.0860.07430.35790.03890.0060.40270.03050.421642.318834.287727.3267
20.92770.4501-0.07830.4218-0.44820.8361-0.05940.12660.04770.01830.0037-0.011-0.11470.1130.05560.31490.01270.01140.39170.03740.466550.13140.188222.068
30.97250.33642.00810.37360.82024.49450.01290.5378-0.07-0.2103-0.04430.159-0.16841.310.03140.41250.2052-0.00290.908-0.07180.273863.096920.14372.8346
43.08392.196.01768.09623.288512.0293-0.24160.34660.2548-1.3289-0.2711-0.1801-0.18581.04660.51280.56430.21980.12930.7245-0.06720.10958.18122.6802-6.8122
50.64780.0055-0.17640.1492-0.10850.68590.02360.07730.0196-0.0759-0.0378-0.03940.19960.03280.01420.44770.0841-0.00110.3763-0.0080.337940.457117.338116.0024
60.69540.1938-0.08910.50340.06160.68770.03450.00750.14770.001-0.0060.01520.0215-0.1163-0.02850.35730.0651-0.00780.40660.04390.419516.411838.622128.27
70.4239-0.40160.81471.1255-0.23175.3106-0.1028-0.1271-0.03520.15660.21110.1492-0.3595-0.0726-0.10830.28130.07750.05560.62390.04550.26461.030428.394756.9423
80.8736-0.0928-0.32890.01650.02910.1303-0.0109-0.05230.0135-0.01990.03860.03990.032-0.0238-0.02770.3933-0.0242-0.03210.46270.05840.377215.350918.196640.4929
90.45260.0927-0.01290.0862-0.19980.61560.0303-0.0604-0.0147-0.03410.0277-0.01220.0541-0.0859-0.0580.39750.0226-0.0230.39750.02310.392423.017820.862839.9828
106.1366.8597-0.76729.3099-3.98636.0690.19690.02450.24680.2217-0.25810.24020.04410.53490.06120.35590.02950.03070.44480.07920.435434.438319.638853.821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 46
2X-RAY DIFFRACTION2A47 - 100
3X-RAY DIFFRACTION3A101 - 149
4X-RAY DIFFRACTION4A150 - 185
5X-RAY DIFFRACTION5A186 - 371
6X-RAY DIFFRACTION6B1 - 103
7X-RAY DIFFRACTION7B104 - 185
8X-RAY DIFFRACTION8B186 - 217
9X-RAY DIFFRACTION9B218 - 366
10X-RAY DIFFRACTION10B367 - 372

+
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://pdbjlvh1.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