[English] 日本語
Yorodumi
- PDB-4a3r: Crystal structure of Enolase from Bacillus subtilis. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a3r
TitleCrystal structure of Enolase from Bacillus subtilis.
ComponentsENOLASE
KeywordsLYASE / GLYCOLYSIS / DEGRADOSOME
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / sporulation resulting in formation of a cellular spore / glycolytic process / magnesium ion binding / cell surface / extracellular region
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / 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
CITRIC ACID / Enolase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNewman, J.A. / Hewitt, L. / Rodrigues, C. / Solovyova, A.S. / Harwood, C.R. / Lewis, R.J.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Dissection of the Network of Interactions that Links RNA Processing with Glycolysis in the Bacillus Subtilis Degradosome.
Authors: Newman, J.A. / Hewitt, L. / Rodrigues, C. / Solovyova, A.S. / Harwood, C.R. / Lewis, R.J.
History
DepositionOct 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_conn.ptnr2_label_seq_id / _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: ENOLASE
B: ENOLASE
C: ENOLASE
D: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,7437
Polymers186,5054
Non-polymers2383
Water14,196788
1
A: ENOLASE
B: ENOLASE

A: ENOLASE
B: ENOLASE

A: ENOLASE
B: ENOLASE

A: ENOLASE
B: ENOLASE


Theoretical massNumber of molelcules
Total (without water)373,0098
Polymers373,0098
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area24070 Å2
ΔGint-46.4 kcal/mol
Surface area107390 Å2
MethodPISA
2
C: ENOLASE
D: ENOLASE
hetero molecules

C: ENOLASE
D: ENOLASE
hetero molecules

C: ENOLASE
D: ENOLASE
hetero molecules

C: ENOLASE
D: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,96220
Polymers373,0098
Non-polymers95212
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area27120 Å2
ΔGint-129 kcal/mol
Surface area105040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.074, 187.074, 56.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9466, 0.3225, -0.007375), (0.3225, -0.9466, -0.001068), (-0.007326, -0.001368, -1)
Vector: -0.00329, -0.06473, -6.69889)

-
Components

#1: Protein
ENOLASE / / 2-PHOSPHO-D-GLYCERATE HYDRO-LYASE / 2-PHOSPHOGLYCERATE DEHYDRATASE


Mass: 46626.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P37869, phosphopyruvate hydratase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 788 / 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: 2.66 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 1.0 M TRI-SODIUM CITRATE 0.1 M, NA CACODYLATE PH 6.5 .

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9804
DetectorType: ADSC CCD / Detector: CCD / Date: May 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 96029 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IYX

1iyx


Resolution: 2.2→19.83 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 4530 5 %
Rwork0.1738 --
obs0.176 90492 90.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.163 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--5.2044 Å20 Å20 Å2
2---5.2044 Å20 Å2
3---10.4088 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13032 0 15 788 13835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813244
X-RAY DIFFRACTIONf_angle_d1.07217929
X-RAY DIFFRACTIONf_dihedral_angle_d14.6934873
X-RAY DIFFRACTIONf_chiral_restr0.072032
X-RAY DIFFRACTIONf_plane_restr0.0042375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.36351110.28952315X-RAY DIFFRACTION74
2.225-2.25110.35691340.25352376X-RAY DIFFRACTION75
2.2511-2.27850.26461220.24692443X-RAY DIFFRACTION78
2.2785-2.30730.29731270.24652492X-RAY DIFFRACTION79
2.3073-2.33760.32831440.23712513X-RAY DIFFRACTION80
2.3376-2.36960.28271240.23612631X-RAY DIFFRACTION83
2.3696-2.40340.29451430.23472747X-RAY DIFFRACTION87
2.4034-2.43920.29321450.22222755X-RAY DIFFRACTION87
2.4392-2.47730.26011380.21662725X-RAY DIFFRACTION87
2.4773-2.51780.28091270.20392859X-RAY DIFFRACTION91
2.5178-2.56110.26361540.20472866X-RAY DIFFRACTION90
2.5611-2.60760.23771710.19632850X-RAY DIFFRACTION92
2.6076-2.65760.23741480.19992942X-RAY DIFFRACTION94
2.6576-2.71180.26411450.23009X-RAY DIFFRACTION95
2.7118-2.77060.24671790.18182940X-RAY DIFFRACTION95
2.7706-2.83480.22771480.18323072X-RAY DIFFRACTION95
2.8348-2.90550.23381630.19033009X-RAY DIFFRACTION97
2.9055-2.98380.2261740.17673033X-RAY DIFFRACTION96
2.9838-3.07130.24011690.17253049X-RAY DIFFRACTION97
3.0713-3.17010.21771500.1723106X-RAY DIFFRACTION97
3.1701-3.28290.21991400.16813094X-RAY DIFFRACTION97
3.2829-3.41370.20821670.1613087X-RAY DIFFRACTION98
3.4137-3.56820.19441460.15163077X-RAY DIFFRACTION97
3.5682-3.75510.19011480.14773098X-RAY DIFFRACTION96
3.7551-3.98860.1741880.1393000X-RAY DIFFRACTION95
3.9886-4.29370.1691680.13142985X-RAY DIFFRACTION94
4.2937-4.72050.15721630.12682986X-RAY DIFFRACTION93
4.7205-5.39150.19041660.14242954X-RAY DIFFRACTION93
5.3915-6.7480.20521660.17152974X-RAY DIFFRACTION92
6.748-19.83060.17461620.15982975X-RAY DIFFRACTION89

+
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