[English] 日本語
Yorodumi
- PDB-2ppg: Crystal structure of putative isomerase from Sinorhizobium meliloti -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ppg
TitleCrystal structure of putative isomerase from Sinorhizobium meliloti
ComponentsPutative isomerase
KeywordsISOMERASE / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


amino acid catabolic process / catalytic activity / magnesium ion binding
Similarity search - Function
Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain ...Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.49 Å
AuthorsRamagopal, U.A. / Toro, R. / Dickey, M. / Logan, C. / Groshong, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative isomerase from Sinorhizobium meliloti.
Authors: Ramagopal, U.A. / Toro, R. / Dickey, M. / Logan, C. / Groshong, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 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 1.6Aug 30, 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 1.7Nov 15, 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: Putative isomerase
B: Putative isomerase
C: Putative isomerase
D: Putative isomerase


Theoretical massNumber of molelcules
Total (without water)176,7684
Polymers176,7684
Non-polymers00
Water2,414134
1
A: Putative isomerase
B: Putative isomerase
C: Putative isomerase
D: Putative isomerase

A: Putative isomerase
B: Putative isomerase
C: Putative isomerase
D: Putative isomerase


Theoretical massNumber of molelcules
Total (without water)353,5358
Polymers353,5358
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area32690 Å2
ΔGint-71 kcal/mol
Surface area93900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.154, 150.829, 147.649
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Putative isomerase /


Mass: 44191.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0374, SMa0708 / Plasmid: BC-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92ZS5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Tris-Bis pH 5.5, 25 % PEG 3350, 0.2 M Ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 51301 / Num. obs: 51301 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.157 / Χ2: 0.935 / Net I/σ(I): 4.8
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.56 / Num. unique all: 9385 / Rsym value: 0.54 / Χ2: 0.656 / % possible all: 95.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: PDB entry 2NQL

2nql


Resolution: 2.49→42 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.411 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.531 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2581 5.1 %RANDOM
Rwork0.183 ---
all0.186 50866 --
obs0.186 50866 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.11 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å20 Å20 Å2
2---1.01 Å20 Å2
3----3.62 Å2
Refinement stepCycle: LAST / Resolution: 2.49→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11656 0 0 134 11790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211925
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.95616179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82951516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89422.481516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.464151920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.99515112
X-RAY DIFFRACTIONr_chiral_restr0.0820.21798
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029103
X-RAY DIFFRACTIONr_nbd_refined0.2090.25809
X-RAY DIFFRACTIONr_nbtor_refined0.3170.38169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.5770
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.521
X-RAY DIFFRACTIONr_mcbond_it2.46127683
X-RAY DIFFRACTIONr_mcangle_it3.716312056
X-RAY DIFFRACTIONr_scbond_it2.66224718
X-RAY DIFFRACTIONr_scangle_it3.78634123
LS refinement shellResolution: 2.49→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 200 -
Rwork0.262 3220 -
obs-3420 91.03 %

+
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