[English] 日本語
Yorodumi
- PDB-4i9f: Crystal structure of glycerol phosphate phosphatase Rv1692 from M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i9f
TitleCrystal structure of glycerol phosphate phosphatase Rv1692 from Mycobacterium tuberculosis in complex with calcium
ComponentsGlycerol 3-phosphate phosphatase
KeywordsHYDROLASE / Haloacid dehalogenase superfamily / phosphatase / glycerol 3-phosphate binding
Function / homology
Function and homology information


glycerol-1-phosphatase activity / glycerophospholipid catabolic process / glycerol metabolic process / cobalt ion binding / phosphatase activity / manganese ion binding / magnesium ion binding / protein homodimerization activity / metal ion binding
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #290 / GCN5-related N-acetyltransferase-like domain / GCN5-related N-acetyltransferase like domain / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / GMP Synthetase; Chain A, domain 3 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily ...GMP Synthetase; Chain A, domain 3 - #290 / GCN5-related N-acetyltransferase-like domain / GCN5-related N-acetyltransferase like domain / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / GMP Synthetase; Chain A, domain 3 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GNAT_like domain-containing protein / D-glycerol 3-phosphate phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsBiswas, T. / Larrouy-Maumus, G. / de Carvalho, L.P. / Tsodikov, O.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Discovery of a glycerol 3-phosphate phosphatase reveals glycerophospholipid polar head recycling in Mycobacterium tuberculosis.
Authors: Larrouy-Maumus, G. / Biswas, T. / Hunt, D.M. / Kelly, G. / Tsodikov, O.V. / de Carvalho, L.P.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycerol 3-phosphate phosphatase
B: Glycerol 3-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3166
Polymers76,1602
Non-polymers1564
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-57 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.814, 70.318, 97.099
Angle α, β, γ (deg.)90.00, 95.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-540-

HOH

-
Components

#1: Protein Glycerol 3-phosphate phosphatase


Mass: 38079.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1731, Rv1692 / Production host: Escherichia coli (E. coli) / References: UniProt: O33194, UniProt: L7N4Y2*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 43.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES (50 mM) pH 7.5 PEG 4000 (10% w/v), Sodium citrate trihydrate (40 mM), and CaCl2 (100 mM), VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 31079 / Num. obs: 30613 / % possible obs: 98.5 % / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PDW

3pdw


Resolution: 2.21→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.084 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24284 1640 5.1 %RANDOM
Rwork0.19102 ---
obs0.19373 30613 97.27 %-
all-31079 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.093 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å2-0.26 Å2
2--0 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.21→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4997 0 4 331 5332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195081
X-RAY DIFFRACTIONr_bond_other_d0.0010.024919
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.966919
X-RAY DIFFRACTIONr_angle_other_deg0.765311233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67623.062209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58415776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5031553
X-RAY DIFFRACTIONr_chiral_restr0.0610.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021125
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.207→2.264 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 80 -
Rwork0.272 1665 -
obs--72.29 %

+
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