[English] 日本語
Yorodumi
- PDB-3ocf: Crystal structure of fumarate lyase:delta crystallin from Brucell... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ocf
TitleCrystal structure of fumarate lyase:delta crystallin from Brucella melitensis in native form
ComponentsFumarate lyase:Delta crystallin
KeywordsLYASE / fumarate lyase / fumarase / brucellosis / orchitis / epididymitis / mastitis / dehydration of fumarate to malate / Kreb's cycle / citric acid cycle / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


aspartate ammonia-lyase / aspartate ammonia-lyase activity / tricarboxylic acid cycle
Similarity search - Function
Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) ...Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fumarate lyase:Delta crystallin
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of fumarate lyase:delta crystallin from Brucella melitensis in native form
Authors: Edwards, T.E. / Arakaki, T.L. / Sankaran, B.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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: Fumarate lyase:Delta crystallin
B: Fumarate lyase:Delta crystallin
C: Fumarate lyase:Delta crystallin
D: Fumarate lyase:Delta crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,30313
Polymers205,8514
Non-polymers4529
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28220 Å2
ΔGint-132 kcal/mol
Surface area53160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.230, 86.460, 105.160
Angle α, β, γ (deg.)90.000, 91.910, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 400
2116B1 - 400
3116C1 - 400
4116D1 - 400
1126A401 - 455
2126B401 - 455
3126C401 - 455

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Fumarate lyase:Delta crystallin


Mass: 51462.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 2308 / Gene: aspA, BAB1_1959 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YLW1, aspartate ammonia-lyase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 1.9 Å3/Da / Density % sol: 35.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 86.6 mg/mL of BrabA.00047.a.A5 PS00511 full lenght tag against JCSG+ condition A9, 0.2 M ammonium chloride, 20% PEG 3350 with 20% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: 86.6 mg/mL of BrabA.00047.a.A5 PS00511 full lenght tag against JCSG+ condition A9, 0.2 M ammonium chloride, 20% PEG 3350 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 215952a9, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 90194 / Num. obs: 89781 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 30.177 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.65
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.150.528218208652298.3
2.15-2.210.4432.619969645499.6
2.21-2.280.3663.320703627899.8
2.28-2.350.3154.122470610599.8
2.35-2.420.2674.922096587699.9
2.42-2.510.2145.921702576699.9
2.51-2.60.1986.720832553199.9
2.6-2.710.1687.819977531799.7
2.71-2.830.1379.319222510099.9
2.83-2.970.11111.218549491999.7
2.97-3.130.09213.317386461199.8
3.13-3.320.06917.416724444899.9
3.32-3.550.0572115433411099.7
3.55-3.830.04426.114511385999.8
3.83-4.20.03630.513352357699.9
4.2-4.70.03233.212021321699.8
4.7-5.420.03532.110610284999.8
5.42-6.640.03928.98975242899.8
6.64-9.390.02738.46837188199.7
9.390.02542.4324193587.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.82 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.73 Å
Translation3 Å19.73 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OCE

3oce


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2049 / WRfactor Rwork: 0.1541 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.86 / SU B: 11.154 / SU ML: 0.134 / SU R Cruickshank DPI: 0.2435 / SU Rfree: 0.1944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 4501 5 %RANDOM
Rwork0.1712 ---
obs0.174 89651 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.7 Å2 / Biso mean: 32.2479 Å2 / Biso min: 9.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-0.49 Å2
2--1.18 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12854 0 24 633 13511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02213133
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9717874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4651765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10524.304539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.183152109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.17115100
X-RAY DIFFRACTIONr_chiral_restr0.0940.22165
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219876
X-RAY DIFFRACTIONr_mcbond_it0.7111.58719
X-RAY DIFFRACTIONr_mcangle_it1.259213897
X-RAY DIFFRACTIONr_scbond_it2.26234414
X-RAY DIFFRACTIONr_scangle_it3.6314.53964
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2800LOOSE POSITIONAL0.235
12B2800LOOSE POSITIONAL0.365
13C2800LOOSE POSITIONAL0.315
14D2800LOOSE POSITIONAL0.325
11A2800LOOSE THERMAL2.5610
12B2800LOOSE THERMAL3.1710
13C2800LOOSE THERMAL3.7310
14D2800LOOSE THERMAL3.2810
21A236LOOSE POSITIONAL0.245
22B236LOOSE POSITIONAL0.285
23C236LOOSE POSITIONAL0.25
21A236LOOSE THERMAL5.6610
22B236LOOSE THERMAL8.3310
23C236LOOSE THERMAL1010
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 346 -
Rwork0.225 6145 -
all-6491 -
obs--98.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.17560.1447-0.07020.2324-0.15170.12760.010.0230.00750.0102-0.02840.00240.0067-0.00030.01840.04990.00170.0080.0871-0.00790.03569.755416.355813.0624
20.33980.110.20370.14450.05820.13450.02570.0037-0.03580.0033-0.0386-0.03560.01680.00710.01290.06210.0050.00970.03290.01260.075928.82351.398841.2894
30.53830.11570.01490.16810.10390.08010.04870.186-0.07660.0598-0.0269-0.05710.0207-0.0323-0.02180.0489-0.0239-0.0340.1159-0.00230.035833.67376.853213.2038
40.11650.0773-0.05240.1537-0.09530.0791-0.0282-0.026-0.00890.00460.0044-0.0043-0.0284-0.00860.02380.07730.0023-0.00270.0494-0.00570.053613.419220.085742.0713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

+
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