[English] 日本語
Yorodumi
- PDB-3sbf: Crystal structure of the mutant P311A of enolase superfamily memb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sbf
TitleCrystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES BACTERIUM complexed with Mg and D-Arabinonate
Componentsmandelate racemase / muconate lactonizing enzyme
KeywordsISOMERASE / enolase fold / acid sugar dehydratase / D-Araninonate
Function / homology
Function and homology information


amino acid catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase-like / 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 ...D-mannonate dehydratase-like / 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
D-arabinonic acid / D-galactonate dehydratase family member VSWAT3_13707
Similarity search - Component
Biological speciesVibrionales bacterium SWAT-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the mutant P311A of enolase superfamily member from Vibrionales bacterium complexed with Mg and D-Arabinonate
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
History
DepositionJun 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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.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_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: mandelate racemase / muconate lactonizing enzyme
B: mandelate racemase / muconate lactonizing enzyme
C: mandelate racemase / muconate lactonizing enzyme
D: mandelate racemase / muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,77615
Polymers181,5134
Non-polymers1,26311
Water25,1671397
1
A: mandelate racemase / muconate lactonizing enzyme
D: mandelate racemase / muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3767
Polymers90,7572
Non-polymers6195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-33 kcal/mol
Surface area28830 Å2
MethodPISA
2
B: mandelate racemase / muconate lactonizing enzyme
C: mandelate racemase / muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4008
Polymers90,7572
Non-polymers6436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-43 kcal/mol
Surface area28530 Å2
MethodPISA
3
A: mandelate racemase / muconate lactonizing enzyme
C: mandelate racemase / muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6148
Polymers90,7572
Non-polymers8576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-22 kcal/mol
Surface area31400 Å2
MethodPISA
4
B: mandelate racemase / muconate lactonizing enzyme
hetero molecules

D: mandelate racemase / muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1627
Polymers90,7572
Non-polymers4055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area2940 Å2
ΔGint-31 kcal/mol
Surface area30730 Å2
MethodPISA
5
A: mandelate racemase / muconate lactonizing enzyme
B: mandelate racemase / muconate lactonizing enzyme
hetero molecules

A: mandelate racemase / muconate lactonizing enzyme
B: mandelate racemase / muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,80016
Polymers181,5134
Non-polymers1,28712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area11320 Å2
ΔGint-28 kcal/mol
Surface area57630 Å2
MethodPISA
6
C: mandelate racemase / muconate lactonizing enzyme
D: mandelate racemase / muconate lactonizing enzyme
hetero molecules

C: mandelate racemase / muconate lactonizing enzyme
D: mandelate racemase / muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,75214
Polymers181,5134
Non-polymers1,23810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area10040 Å2
ΔGint-34 kcal/mol
Surface area57310 Å2
MethodPISA
7
A: mandelate racemase / muconate lactonizing enzyme
B: mandelate racemase / muconate lactonizing enzyme
C: mandelate racemase / muconate lactonizing enzyme
D: mandelate racemase / muconate lactonizing enzyme
hetero molecules

A: mandelate racemase / muconate lactonizing enzyme
B: mandelate racemase / muconate lactonizing enzyme
C: mandelate racemase / muconate lactonizing enzyme
D: mandelate racemase / muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,55230
Polymers363,0278
Non-polymers2,52522
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area51320 Å2
ΔGint-179 kcal/mol
Surface area84980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.372, 163.372, 110.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-427-

HOH

21B-1360-

HOH

31C-1238-

HOH

41C-1313-

HOH

51D-481-

HOH

61D-1344-

HOH

71D-1355-

HOH

-
Components

#1: Protein
mandelate racemase / muconate lactonizing enzyme


Mass: 45378.359 Da / Num. of mol.: 4 / Fragment: unp residues 2-399 / Mutation: P311A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrionales bacterium SWAT-3 (bacteria)
Gene: VSWAT3_13707 / Production host: Escherichia coli (E. coli) / References: UniProt: A5KUH4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-D8T / D-arabinonic acid


Mass: 166.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1397 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 3350, 0.1M Hepes, 0.2M Proline, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→46.794 Å / Num. all: 232178 / Num. obs: 232178 / % possible obs: 98.27 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3R25

3r25


Resolution: 1.5→46.794 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 11637 5.01 %RANDOM
Rwork0.1797 ---
all0.1811 232178 --
obs0.1811 232178 98.27 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.946 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7497 Å20 Å2-0 Å2
2--0.7497 Å2-0 Å2
3----1.4994 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12618 0 79 1397 14094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613066
X-RAY DIFFRACTIONf_angle_d1.06517781
X-RAY DIFFRACTIONf_dihedral_angle_d13.4384816
X-RAY DIFFRACTIONf_chiral_restr0.0741920
X-RAY DIFFRACTIONf_plane_restr0.0062330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.40332580.36974916X-RAY DIFFRACTION66
1.517-1.53490.36073320.34456648X-RAY DIFFRACTION90
1.5349-1.55360.34143950.32367333X-RAY DIFFRACTION99
1.5536-1.57330.31354230.29357331X-RAY DIFFRACTION100
1.5733-1.5940.28873770.26367411X-RAY DIFFRACTION100
1.594-1.61580.28753570.25267473X-RAY DIFFRACTION100
1.6158-1.63890.28663800.24177404X-RAY DIFFRACTION100
1.6389-1.66340.26384230.22317385X-RAY DIFFRACTION100
1.6634-1.68940.25514050.21847405X-RAY DIFFRACTION100
1.6894-1.71710.2463940.20857429X-RAY DIFFRACTION100
1.7171-1.74670.25764010.20547394X-RAY DIFFRACTION100
1.7467-1.77840.22544360.20147430X-RAY DIFFRACTION100
1.7784-1.81260.24144130.19547385X-RAY DIFFRACTION100
1.8126-1.84960.25353690.19947423X-RAY DIFFRACTION100
1.8496-1.88990.26333820.19967457X-RAY DIFFRACTION100
1.8899-1.93380.21983590.19417514X-RAY DIFFRACTION100
1.9338-1.98220.2394020.19267389X-RAY DIFFRACTION100
1.9822-2.03580.24674110.19487443X-RAY DIFFRACTION100
2.0358-2.09570.23673850.19247445X-RAY DIFFRACTION100
2.0957-2.16330.22733920.19147429X-RAY DIFFRACTION100
2.1633-2.24060.22613940.18717440X-RAY DIFFRACTION99
2.2406-2.33040.23573640.18047447X-RAY DIFFRACTION99
2.3304-2.43640.21243940.18567422X-RAY DIFFRACTION99
2.4364-2.56490.21514040.18047433X-RAY DIFFRACTION99
2.5649-2.72550.20613650.18327488X-RAY DIFFRACTION99
2.7255-2.93590.21583830.18317492X-RAY DIFFRACTION99
2.9359-3.23130.18613850.17117566X-RAY DIFFRACTION100
3.2313-3.69880.16614050.14887582X-RAY DIFFRACTION100
3.6988-4.65940.14214350.13457647X-RAY DIFFRACTION100
4.6594-46.81640.16714140.15187980X-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://pdbjlvh1.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