[English] 日本語
Yorodumi
- PDB-4apa: Crystal structure of Mycobacterium tuberculosis fumarase (Rv1098c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4apa
TitleCrystal structure of Mycobacterium tuberculosis fumarase (Rv1098c) S318A in apo form
ComponentsFUMARATE HYDRATASE CLASS II
KeywordsHYDROLASE / METABOLISM
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytosol
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 / Ribonucleotide Reductase Protein R1; domain 1 ...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 / 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 hydratase class II / Fumarate hydratase class II
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBellinzoni, M. / Haouz, A. / Mechaly, A.E. / Alzari, P.M.
CitationJournal: FEBS Lett. / Year: 2012
Title: Conformational Changes Upon Ligand Binding in the Essential Class II Fumarase Rv1098C from Mycobacterium Tuberculosis.
Authors: Mechaly, A.E. / Haouz, A. / Miras, I. / Barilone, N. / Weber, P. / Shepard, W. / Alzari, P.M. / Bellinzoni, M.
History
DepositionMar 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FUMARATE HYDRATASE CLASS II
B: FUMARATE HYDRATASE CLASS II
C: FUMARATE HYDRATASE CLASS II
D: FUMARATE HYDRATASE CLASS II


Theoretical massNumber of molelcules
Total (without water)200,4074
Polymers200,4074
Non-polymers00
Water14,376798
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24370 Å2
ΔGint-136.9 kcal/mol
Surface area53820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.270, 97.142, 96.436
Angle α, β, γ (deg.)90.00, 104.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.876, -0.0093, -0.4823), (-0.0099, -1, 0.0013), (-0.4823, 0.0037, -0.876)11.4582, -97.5254, 46.377
2given(-0.9289, 0.2578, 0.2657), (0.2501, -0.0922, 0.9638), (0.273, 0.9618, 0.0212)-89.5637, -76.6873, 95.9257
3given(-0.9427, -0.2515, 0.2192), (-0.2491, 0.0939, -0.9639), (0.2218, -0.9633, -0.1511)-113.3202, -20.4331, 6.4166

-
Components

#1: Protein
FUMARATE HYDRATASE CLASS II / FUMARASE C


Mass: 50101.660 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: O53446, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 318 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 318 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 318 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 318 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 318 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 318 TO ALA
Sequence detailsN-TER GLY IS A PURIFICATION TAG LEFTOVER

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.5 % / Description: NONE
Crystal growpH: 8 / Details: 20% PEG 8000, 0.2 M CACL2, 0.1 M TRIS-HCL PH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.04→43.41 Å / Num. obs: 148043 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 29.34 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 2.04→2.16 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.3 / % possible all: 86.8

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ADL

4adl


Resolution: 2.04→43.41 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9376 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.129 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.112
Details: NCS REPRESENTATION: RESTRAINT LSSR SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. NUMBER OF LIBRARIES USED: 8
RfactorNum. reflection% reflectionSelection details
Rfree0.1791 7424 5.01 %RANDOM
Rwork0.1654 ---
obs0.1661 148043 97.15 %-
Displacement parametersBiso mean: 34.21 Å2
Baniso -1Baniso -2Baniso -3
1-5.6417 Å20 Å23.8676 Å2
2--1.056 Å20 Å2
3----6.6977 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: LAST / Resolution: 2.04→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12898 0 0 798 13696
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113078HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9717823HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6044SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes330HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1959HARMONIC5
X-RAY DIFFRACTIONt_it13078HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion2.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1856SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16745SEMIHARMONIC4
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 405 5 %
Rwork0.2064 7693 -
all0.2079 8098 -
obs--97.15 %
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)
1-0.25250.32320.38350-0.78870.7965-0.00480.0012-0.05970.0427-0.01240.02560.045-0.04640.0172-0.0409-0.0040.00520.10160.2485-0.1113-37.8626-65.01577.6373
25.48330.32560.46920.7632-1.37953.04250.015-0.6908-0.35150.1975-0.0605-0.04830.0201-0.00030.0455-0.0270.0286-0.01510.01270.0525-0.0367-40.2061-59.932767.7819
32.4252-0.2108-0.13710.19290.18671.0342-0.0579-0.3788-0.27950.08430.0422-0.04620.18830.19760.0157-0.09560.0559-0.0506-0.02710.0478-0.0372-25.7901-59.786161.8357
40.6663-0.01360.26080.34560.05150.61660.0060.0079-0.0473-0.03110.0506-0.1596-0.00390.1407-0.0566-0.09220.0129-0.0014-0.02820.0170.0083-29.0459-58.283637.688
50.4132-0.030.08230.1075-0.16940.4870.01860.0124-0.0553-0.04140.0003-0.12910.03810.069-0.019-0.07890.0136-0.0098-0.01660.01680.005-33.8094-59.097735.473
60.586-0.04240.17320.4760.06020.50420.0292-0.05960.03860.0451-0.0272-0.1079-0.01630.0262-0.0019-0.16090.0079-0.0163-0.10770.0292-0.1069-40.5854-56.450842.093
71.8531-0.05832.12372.0084-0.76118.4815-0.08490.4259-0.0773-0.67380.06060.12460.0053-0.2720.0244-0.00210.0143-0.02310.0057-0.0774-0.1513-46.3803-70.98520.4002
81.71541.8917-3.31330.1489-0.28590.0487-0.01430.342-0.0225-0.32160.0124-0.01980.05820.02760.00190.05880.09740.04580.0688-0.0422-0.2091-37.0223-69.3756-5.929
95.39883.73312.7132.4537-0.60416.03850.061-0.12720.04370.010.03670.0775-0.07270.0647-0.09770.0430.0055-0.0287-0.03690.0822-0.0337-59.9971-35.6251-3.1986
100.8862-0.02490.56240.4191-0.23552.42990.06150.12620.2588-0.2938-0.0257-0.0088-0.03020.0297-0.03580.018-0.0218-0.0492-0.08580.075-0.0785-54.7115-36.26927.8034
111.99020.5244-0.44770.7488-0.43511.0979-0.11920.35420.2832-0.3250.0557-0.0866-0.07280.07650.06350.0509-0.06430.01120.01210.0908-0.0814-40.1556-37.45794.0215
120.42340.03060.01140.6040.35531.2256-0.00350.11560.0604-0.14540.0715-0.1953-0.07720.182-0.0679-0.0859-0.03160.0172-0.04170.0383-0.0014-31.7395-38.856227.0417
130.4110.01840.05960.28310.21190.83990.01810.06620.0814-0.12680.0069-0.1127-0.11480.0563-0.025-0.0814-0.0180.0025-0.05440.0424-0.023-38.8692-39.407330.3642
140.8734-0.37731.15251.04250.13233.6571-0.0345-0.05830.31320.06150.024-0.0818-0.2679-0.01190.0105-0.1032-0.0685-0.0176-0.09620.00230.0674-32.3761-23.088449.9971
153.57150.0609-2.63433.2477-0.159912.3526-0.0208-0.4701-0.10320.70440.02590.00950.25420.3941-0.0050.0408-0.0095-0.12940.0272-0.1077-0.1638-25.2938-27.733178.4383
16-0.6536-2.01021.35261.1277-0.8150.7456-0.1176-0.09510.16310.13340.1793-0.06360.0960.0878-0.0617-0.1298-0.0642-0.12670.0206-0.07670.0317-18.4614-29.544465.8499
170.0136-0.2238-0.02450.7753-0.336-0.0136-0.00470.05420.02380.0106-0.0018-0.0021-0.02260.01730.00660.07810.06220.1018-0.19080.28170.1063-50.0943-5.225125.8479
185.4377-2.4587-0.32562.3908-0.65880.50280.04320.40650.7417-0.0361-0.0601-0.4071-0.22490.00050.017-0.0111-0.03620.0075-0.07330.0660.0141-50.5373-17.367428.3773
191.3046-1.3209-0.75663.15881.65561.75230.0490.08150.2292-0.11790.01250.0357-0.1783-0.0935-0.0615-0.0352-0.0089-0.016-0.07350.04010.045-71.0198-16.533136.8458
201.8275-0.6446-0.36221.33020.09540.33770.03690.1270.2624-0.05310.0138-0.1241-0.09460.0176-0.0508-0.0364-0.0018-0.0164-0.11160.04560.0139-61.5709-17.569633.5331
210.2253-0.1553-0.04791.35180.45840.4184-0.00540.0219-0.0008-0.0535-0.01250.1318-0.012-0.03520.0179-0.0327-0.0037-0.0347-0.02280.02880.0473-68.7251-49.909430.5679
220.3134-0.103-0.03711.3150.31550.180.01450.04240.0564-0.1060.01050.0375-0.05430.002-0.025-0.04610.0019-0.026-0.04770.0381-0.0174-63.7945-45.482630.0715
230.4510.0446-0.05541.04410.13260.5098-0.01890.02830.0452-0.1517-0.0030.0288-0.08290.01220.0218-0.10750.0164-0.0168-0.11580.0432-0.0673-58.3332-45.542626.7503
243.7482-1.0114-0.55143.51120.74261.7077-0.0652-0.0162-0.2701-0.01090.01150.02490.21980.06250.05370.03270.0032-0.0274-0.0596-0.00380.0067-67.058-88.927216.7119
25-0.22360.19310.40341.4037-0.40540.2253-0.0051-0.0174-0.0229-0.0410.0129-0.00810.03620.0219-0.00780.10960.0012-0.061-0.17490.15530.0852-45.0628-91.887146.4429
264.83031.5081-0.51624.3173-1.15672.2224-0.0492-0.3047-0.5917-0.0657-0.1615-0.1840.25880.23320.2107-0.01720.0636-0.0068-0.02430.04260.0711-45.532-81.073545.1113
272.01930.80810.58731.73440.56042.1193-0.0853-0.231-0.1890.1108-0.03460.14960.1934-0.13990.1199-0.0454-0.00320.0461-0.11740.0022-0.0413-66.6134-79.438548.4695
282.66540.7781-0.7091.2579-0.34420.6901-0.0642-0.2112-0.31560.1744-0.0275-0.05840.04970.08280.0917-0.01320.0292-0.006-0.08980.0385-0.0292-55.8567-78.851448.8783
290.39170.155-0.01261.59750.20750.3766-0.0088-0.0192-0.00050.1347-0.00350.13250.0351-0.02730.0123-0.03330.00050.002-0.01510.01990.0055-61.6051-51.587552.8958
300.9296-0.4512-1.21491.12440.74852.5348-0.02050.1381-0.0287-0.1144-0.08970.1721-0.104-0.04370.1102-0.0466-0.0197-0.0109-0.0531-0.00490.0237-72.4342-71.742741.6332
310.49820.48730.44721.65770.95631.23270.0402-0.06310.00190.1162-0.0247-0.07010.044-0.0083-0.0155-0.0660.0153-0.0121-0.06430.0258-0.0279-54.347-46.275250.7016
320.4326-0.1355-0.01791.04210.22480.82620.0017-0.0507-0.0120.12470.0548-0.04820.04720.032-0.0565-0.09790.0015-0.0152-0.08940.0348-0.0448-51.9057-51.992650.7496
334.241.4815-1.077310.2246-0.02711.39410.0325-0.03740.7620.38860.1063-0.144-0.25080.111-0.13880.01250.0118-0.0006-0.1493-0.03710.039-54.552-8.258563.8994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 9-13
2X-RAY DIFFRACTION2CHAIN A AND RESID 20-44
3X-RAY DIFFRACTION3CHAIN A AND RESID 45-121
4X-RAY DIFFRACTION4CHAIN A AND RESID 122-242
5X-RAY DIFFRACTION5CHAIN A AND RESID 243-314
6X-RAY DIFFRACTION6CHAIN A AND RESID 325-380
7X-RAY DIFFRACTION7CHAIN A AND RESID 381-444
8X-RAY DIFFRACTION8CHAIN A AND RESID 449-467
9X-RAY DIFFRACTION9CHAIN B AND RESID 9-19
10X-RAY DIFFRACTION10CHAIN B AND RESID 20-48
11X-RAY DIFFRACTION11CHAIN B AND RESID 49-121
12X-RAY DIFFRACTION12CHAIN B AND RESID 122-242
13X-RAY DIFFRACTION13CHAIN B AND RESID 243-377
14X-RAY DIFFRACTION14CHAIN B AND RESID 378-406
15X-RAY DIFFRACTION15CHAIN B AND RESID 407-455
16X-RAY DIFFRACTION16CHAIN B AND RESID 456-466
17X-RAY DIFFRACTION17CHAIN C AND RESID 9-14
18X-RAY DIFFRACTION18CHAIN C AND RESID 20-48
19X-RAY DIFFRACTION19CHAIN C AND RESID 49-77
20X-RAY DIFFRACTION20CHAIN C AND RESID 78-149
21X-RAY DIFFRACTION21CHAIN C AND RESID 150-241
22X-RAY DIFFRACTION22CHAIN C AND RESID 242-325
23X-RAY DIFFRACTION23CHAIN C AND RESID 326-399
24X-RAY DIFFRACTION24CHAIN C AND RESID 400-467
25X-RAY DIFFRACTION25CHAIN D AND RESID 9-14
26X-RAY DIFFRACTION26CHAIN D AND RESID 20-44
27X-RAY DIFFRACTION27CHAIN D AND RESID 45-77
28X-RAY DIFFRACTION28CHAIN D AND RESID 78-121
29X-RAY DIFFRACTION29CHAIN D AND RESID 122-222
30X-RAY DIFFRACTION30CHAIN D AND RESID 223-259
31X-RAY DIFFRACTION31CHAIN D AND RESID 260-314
32X-RAY DIFFRACTION32CHAIN D AND RESID 325-398
33X-RAY DIFFRACTION33CHAIN D AND RESID 399-467

+
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