[English] 日本語
Yorodumi
- PDB-3ovg: The crystal structure of an amidohydrolase from Mycoplasma synovi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ovg
TitleThe crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound
Componentsamidohydrolase
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / amidohydrolases / HAD / PSI / SGX / Zn
Function / homology
Function and homology information


5-phospho-D-xylono-1,4-lactonase / 1,4-lactonase / 1,4-lactonase activity / catabolic process / zinc ion binding
Similarity search - Function
Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phospho-furanose lactonase
Similarity search - Component
Biological speciesMycoplasma synoviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.059 Å
AuthorsZhang, Z. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound
Authors: Zhang, Z. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)248,20224
Polymers246,8486
Non-polymers1,35518
Water21,3481185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19240 Å2
ΔGint-610 kcal/mol
Surface area67840 Å2
MethodPISA
2
A: amidohydrolase
B: amidohydrolase
E: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,10112
Polymers123,4243
Non-polymers6779
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-283 kcal/mol
Surface area36990 Å2
MethodPISA
3
A: amidohydrolase
F: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7348
Polymers82,2832
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-188 kcal/mol
Surface area26180 Å2
MethodPISA
4
B: amidohydrolase
C: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7348
Polymers82,2832
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-188 kcal/mol
Surface area26220 Å2
MethodPISA
5
C: amidohydrolase
D: amidohydrolase
F: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,10112
Polymers123,4243
Non-polymers6779
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-281 kcal/mol
Surface area36730 Å2
MethodPISA
6
D: amidohydrolase
E: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7348
Polymers82,2832
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-190 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.256, 89.186, 96.059
Angle α, β, γ (deg.)98.95, 92.89, 119.86
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
amidohydrolase


Mass: 41141.273 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma synoviae (bacteria) / Strain: 53 / Gene: had, MS53_0025 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli)
Strain (production host): Bl21(de3)+codon+ril (p) Stratagene
References: UniProt: Q4A724
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1185 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M Sodium malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.059→50 Å / Num. obs: 152064 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 4.9
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.9 / Num. unique all: 14991 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MSR

3msr


Resolution: 2.059→43.747 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 7629 5.02 %RANDOM
Rwork0.1724 ---
obs0.1743 151931 97.75 %-
all-152064 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.748 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 19.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.2092 Å20.8013 Å2-0.2209 Å2
2---0.2518 Å20.6802 Å2
3---0.461 Å2
Refinement stepCycle: LAST / Resolution: 2.059→43.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16602 0 42 1185 17829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416989
X-RAY DIFFRACTIONf_angle_d1.41722940
X-RAY DIFFRACTIONf_dihedral_angle_d18.5456348
X-RAY DIFFRACTIONf_chiral_restr0.0962586
X-RAY DIFFRACTIONf_plane_restr0.0082933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.059-2.08240.30041930.21254288X-RAY DIFFRACTION86
2.0824-2.10690.24152670.1874697X-RAY DIFFRACTION97
2.1069-2.13260.23182490.17744872X-RAY DIFFRACTION97
2.1326-2.15960.23082280.17884707X-RAY DIFFRACTION97
2.1596-2.1880.24652630.17384820X-RAY DIFFRACTION97
2.188-2.2180.22712430.16844781X-RAY DIFFRACTION97
2.218-2.24960.22582610.17324794X-RAY DIFFRACTION97
2.2496-2.28320.22792740.17414809X-RAY DIFFRACTION97
2.2832-2.31890.25532570.16764697X-RAY DIFFRACTION98
2.3189-2.35690.21722500.16714846X-RAY DIFFRACTION97
2.3569-2.39750.20922680.16454816X-RAY DIFFRACTION98
2.3975-2.44110.21642430.16324783X-RAY DIFFRACTION98
2.4411-2.48810.20512530.16794889X-RAY DIFFRACTION98
2.4881-2.53890.21422650.16764780X-RAY DIFFRACTION98
2.5389-2.59410.19572380.16234820X-RAY DIFFRACTION98
2.5941-2.65440.23582490.17054837X-RAY DIFFRACTION98
2.6544-2.72080.21882370.1724895X-RAY DIFFRACTION98
2.7208-2.79430.21692530.17184818X-RAY DIFFRACTION98
2.7943-2.87650.21892470.18194876X-RAY DIFFRACTION99
2.8765-2.96940.23252550.18114803X-RAY DIFFRACTION98
2.9694-3.07550.21852840.18834855X-RAY DIFFRACTION99
3.0755-3.19860.21982490.18834879X-RAY DIFFRACTION99
3.1986-3.34410.21622450.18324818X-RAY DIFFRACTION99
3.3441-3.52030.19082410.16844885X-RAY DIFFRACTION99
3.5203-3.74080.18812610.16874894X-RAY DIFFRACTION99
3.7408-4.02940.18262900.15854829X-RAY DIFFRACTION99
4.0294-4.43460.19652700.15434865X-RAY DIFFRACTION99
4.4346-5.07540.17152660.14624856X-RAY DIFFRACTION99
5.0754-6.39130.18622730.17284919X-RAY DIFFRACTION99
6.3913-43.7570.18712570.17894874X-RAY DIFFRACTION100

+
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