[English] 日本語
Yorodumi
- PDB-3rrp: Crystal structure of fumarate hydratase Fum from Mycobacterium ab... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rrp
TitleCrystal structure of fumarate hydratase Fum from Mycobacterium abscessus with malate bound
ComponentsProbable fumarate hydratase Fum
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / tuberculosis / fumerate / malic acid
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Fumarate hydratase, class II / 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 / Fumarase/aspartase (N-terminal domain) ...Fumarate hydratase, class II / 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 / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / 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
(2S)-2-hydroxybutanedioic acid / Fumarate hydratase class II
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Probable fumarate hydratase Fum
B: Probable fumarate hydratase Fum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8217
Polymers99,3672
Non-polymers4545
Water9,692538
1
A: Probable fumarate hydratase Fum
B: Probable fumarate hydratase Fum
hetero molecules

A: Probable fumarate hydratase Fum
B: Probable fumarate hydratase Fum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,64214
Polymers198,7334
Non-polymers90910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area33070 Å2
ΔGint-173 kcal/mol
Surface area51500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.800, 156.920, 57.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-540-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 8 - 463 / Label seq-ID: 12 - 467

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Probable fumarate hydratase Fum


Mass: 49683.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_1250c / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MKP6
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MyabA.01507.a.A1 PW30392 at 29.54 mg/mL against Wizard III/IV screen condition G8, 2.1 M DL Malic acid, pH 7.0 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220029g8, ...Details: MyabA.01507.a.A1 PW30392 at 29.54 mg/mL against Wizard III/IV screen condition G8, 2.1 M DL Malic acid, pH 7.0 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220029g8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 40352 / Num. obs: 39296 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 24.91 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 11.37
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.3-2.364.80.5273.19129432719271993.1
2.36-2.420.5093.5214458274695.1
2.42-2.490.4334.1914315264095.5
2.49-2.570.3874.7214090264197.1
2.57-2.660.3735.0114082257197.1
2.66-2.750.325.9213558247597
2.75-2.850.2487.2813608240598.5
2.85-2.970.2188.2113442234398.8
2.97-3.10.1859.4413007224898.9
3.1-3.250.15511.2712459217698.7
3.25-3.430.12613.8211701204798.5
3.43-3.640.10915.7910969191696.6
3.64-3.890.08519.619565177695.9
3.89-4.20.07222.19763169697.6
4.2-4.60.06124.29396159799.3
4.6-5.140.06322.668573146599.8
5.14-5.940.07518.8375751304100
5.94-7.270.06420.686340112599.9
7.27-10.290.03731.36505788499.8
10.290.03332.16273752298.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.97 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å47.41 Å
Translation3 Å47.41 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 3RD8

3rd8


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.1759 / WRfactor Rwork: 0.1381 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8895 / SU B: 11.986 / SU ML: 0.133 / SU R Cruickshank DPI: 0.3667 / SU Rfree: 0.2174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1950 5 %RANDOM
Rwork0.1601 ---
obs0.1624 39144 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.54 Å2 / Biso mean: 17.2985 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---0.94 Å20 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6761 0 30 538 7329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226892
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9779377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47425.373268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.514151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1831538
X-RAY DIFFRACTIONr_chiral_restr0.090.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215158
X-RAY DIFFRACTIONr_mcbond_it0.4711.54594
X-RAY DIFFRACTIONr_mcangle_it0.83527338
X-RAY DIFFRACTIONr_scbond_it1.70732298
X-RAY DIFFRACTIONr_scangle_it2.7444.52037
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3307 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.150.5
MEDIUM THERMAL0.592
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 129 -
Rwork0.186 2577 -
all-2706 -
obs--92.8 %
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)
10.4182-0.0762-0.13840.74850.05190.7609-0.00680.02240.078-0.00830.00330.0431-0.083-0.16140.00350.02610.03210.00730.04540.00790.0679-14.171331.627-20.2422
20.3187-0.0977-0.03930.78190.08180.48750.0073-0.02710.05250.02470.01770.0481-0.0349-0.0706-0.02510.03870.02640.00710.0425-0.00360.0312-12.222528.9393-6.004
30.00630.0342-0.01030.2141-0.02730.09930.0022-0.01740.00230.0169-0.01610.01930.0049-0.01590.01390.04220.00160.00540.04760.00120.0486-11.0224-0.476-9.4018
40.8804-0.7733-0.0362.07150.09050.376-0.0277-0.0824-0.17360.0650.04030.11660.0954-0.0438-0.01260.0601-0.0360.00590.0430.01440.0353-14.2933-36.642-8.889
53.7703-1.2749-2.94958.7989-2.14163.35870.1534-0.04160.23950.1438-0.0186-0.2943-0.1792-0.0456-0.13480.0203-0.0195-0.02430.1532-0.01730.1196-43.06270.0032-21.7184
60.59320.07020.16620.3179-0.0030.7559-0.0430.00890.0372-0.00870.00290.0354-0.0572-0.07130.04010.01170.0051-0.00510.03580.00940.0614-32.79043.6362-34.4327
70.08440.06610.03020.10680.01250.0724-0.01620.01310.0149-0.00040.00450.021-0.0243-0.01540.01170.045-0.00090.00210.03540.00350.0431.261512.6263-35.0704
85.19930.4995-0.7871.059-0.03372.4081-0.04220.32420.0412-0.0355-0.0418-0.0862-0.14980.06750.0840.0282-0.01120.01880.02390.0080.071539.991724.6849-36.8983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 51
2X-RAY DIFFRACTION2A52 - 158
3X-RAY DIFFRACTION3A159 - 379
4X-RAY DIFFRACTION4A380 - 467
5X-RAY DIFFRACTION5B6 - 18
6X-RAY DIFFRACTION6B19 - 142
7X-RAY DIFFRACTION7B143 - 426
8X-RAY DIFFRACTION8B427 - 465

+
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