[English] 日本語
Yorodumi
- PDB-3mpo: The crystal structure of a hydrolase from Lactobacillus brevis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mpo
TitleThe crystal structure of a hydrolase from Lactobacillus brevis
ComponentsPredicted hydrolase of the HAD superfamily
KeywordsHYDROLASE / SGX / PSI / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


phosphatase activity / magnesium ion binding / cytosol
Similarity search - Function
Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical cof family signature 2. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily ...Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical cof family signature 2. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Predicted hydrolase of the HAD superfamily
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of a hydrolase from Lactobacillus brevis
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Predicted hydrolase of the HAD superfamily
B: Predicted hydrolase of the HAD superfamily
C: Predicted hydrolase of the HAD superfamily
D: Predicted hydrolase of the HAD superfamily


Theoretical massNumber of molelcules
Total (without water)124,8474
Polymers124,8474
Non-polymers00
Water2,072115
1
A: Predicted hydrolase of the HAD superfamily


Theoretical massNumber of molelcules
Total (without water)31,2121
Polymers31,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Predicted hydrolase of the HAD superfamily


Theoretical massNumber of molelcules
Total (without water)31,2121
Polymers31,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Predicted hydrolase of the HAD superfamily


Theoretical massNumber of molelcules
Total (without water)31,2121
Polymers31,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Predicted hydrolase of the HAD superfamily


Theoretical massNumber of molelcules
Total (without water)31,2121
Polymers31,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.254, 108.254, 130.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Predicted hydrolase of the HAD superfamily


Mass: 31211.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / JCM 1170) / Gene: HAD, LVIS_0481 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli)
Strain (production host): BL21 (DE3)-Codon+RIL (p)-stratagene
References: UniProt: Q03T33
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 4% Tacsimate pH 4.0, 12% w/v Polythylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 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: 2.9→130.7 Å / Num. obs: 28778 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 53.6 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 10.2 / Num. unique all: 4123 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→54.127 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.18 / Phase error: 28.16 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 1460 5.08 %RANDOM
Rwork0.2263 ---
obs0.2293 28713 99.89 %-
all-28778 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.761 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1--13.62 Å20 Å20 Å2
2--0.9487 Å2-0 Å2
3---12.6714 Å2
Refinement stepCycle: LAST / Resolution: 2.9→54.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 0 0 115 7803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067795
X-RAY DIFFRACTIONf_angle_d0.96710572
X-RAY DIFFRACTIONf_dihedral_angle_d18.7032806
X-RAY DIFFRACTIONf_chiral_restr0.061252
X-RAY DIFFRACTIONf_plane_restr0.0041360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00360.34531420.26372688X-RAY DIFFRACTION100
3.0036-3.12390.39751420.2632684X-RAY DIFFRACTION100
3.1239-3.2660.30871390.24672691X-RAY DIFFRACTION100
3.266-3.43820.27891400.23312706X-RAY DIFFRACTION100
3.4382-3.65360.31351620.23432658X-RAY DIFFRACTION100
3.6536-3.93560.27291210.21432742X-RAY DIFFRACTION100
3.9356-4.33150.24891420.1872723X-RAY DIFFRACTION100
4.3315-4.95790.20851580.17072738X-RAY DIFFRACTION100
4.9579-6.2450.26611450.21152755X-RAY DIFFRACTION100
6.245-54.13640.25381690.22852868X-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