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- PDB-7d2r: Crystal structure of Agrobacterium tumefaciens aconitase X mutant... -

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Basic information

Entry
Database: PDB / ID: 7d2r
TitleCrystal structure of Agrobacterium tumefaciens aconitase X mutant - S449C/C510V
Componentscis-3-hydroxy-L-proline dehydratase
KeywordsLYASE / cis-3-hydroxy-L-proline dehydratase
Function / homologyFE2/S2 (INORGANIC) CLUSTER
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsMurase, Y. / Watanabe, Y. / Watanabe, S.
CitationJournal: Commun Biol / Year: 2021
Title: Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.
Authors: Watanabe, S. / Murase, Y. / Watanabe, Y. / Sakurai, Y. / Tajima, K.
History
DepositionSep 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cis-3-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9394
Polymers60,6481
Non-polymers2913
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-14 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.760, 72.678, 58.986
Angle α, β, γ (deg.)90.000, 99.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cis-3-hydroxy-L-proline dehydratase


Mass: 60648.082 Da / Num. of mol.: 1 / Mutation: S449C, C510V
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, sodium chloride, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.404 Å / Num. obs: 59959 / % possible obs: 99.6 % / Redundancy: 3.484 % / Biso Wilson estimate: 40.168 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.095 / Χ2: 1.113 / Net I/σ(I): 9.67 / Num. measured all: 208868
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.133.360.7071.4732494979696710.930.84398.7
2.13-2.273.5190.4662.4232118914791280.8040.5599.8
2.27-2.453.510.293.8429769848984810.9180.34399.9
2.45-2.693.40.25.4426563783878130.950.23899.7
2.69-33.6040.1268.9125369705170390.9820.14899.8
3-3.473.4230.07314.4521448629362650.9940.08799.6
3.47-4.243.6270.04623.5618968525052300.9970.05499.6
4.24-5.973.470.03828.0914070406840550.9980.04599.7
5.97-45.4043.5440.0334.228069228822770.9990.03699.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.005→45.404 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 2879 4.8 %
Rwork0.1875 57070 -
obs0.1895 59949 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 37.8307 Å2 / Biso min: 18.72 Å2
Refinement stepCycle: final / Resolution: 2.005→45.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 11 217 4322
Biso mean--34.41 38.51 -
Num. residues----558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0051-2.03790.32391520.3044272098
2.0379-2.07310.37191230.2939270499
2.0731-2.11080.32451400.27982732100
2.1108-2.15140.27971450.26742644100
2.1514-2.19530.28371640.25452729100
2.1953-2.2430.28841650.24122675100
2.243-2.29520.32011270.25092755100
2.2952-2.35260.28181300.23252744100
2.3526-2.41620.23851370.23282700100
2.4162-2.48730.24811350.22292705100
2.4873-2.56760.25471240.22222738100
2.5676-2.65930.27661530.21692705100
2.6593-2.76580.22511720.2122694100
2.7658-2.89160.27631160.2082752100
2.8916-3.04410.2651440.20292722100
3.0441-3.23470.24391220.19942721100
3.2347-3.48440.26531380.17932721100
3.4844-3.83490.21461130.16312717100
3.8349-4.38940.1791350.14152709100
4.3894-5.52860.15051140.13662748100
5.5286-45.4040.171300.14072735100

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