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- PDB-7cnp: Crystal structure of Agrobacterium tumefaciens aconitase X (apo-form) -

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Basic information

Entry
Database: PDB / ID: 7cnp
TitleCrystal structure of Agrobacterium tumefaciens aconitase X (apo-form)
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 / SAD / Resolution: 1.6 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
DepositionAug 3, 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
B: cis-3-hydroxy-L-proline dehydratase
C: cis-3-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,5089
Polymers181,9083
Non-polymers6006
Water38,3722130
1
A: cis-3-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8363
Polymers60,6361
Non-polymers2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-16 kcal/mol
Surface area19530 Å2
MethodPISA
2
B: cis-3-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8363
Polymers60,6361
Non-polymers2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-16 kcal/mol
Surface area19770 Å2
MethodPISA
3
C: cis-3-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8363
Polymers60,6361
Non-polymers2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-16 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.131, 73.150, 133.603
Angle α, β, γ (deg.)90.000, 101.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 60636.035 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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.: 3 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2130 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, magnesium chloride, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→45.556 Å / Num. obs: 342014 / % possible obs: 95.4 % / Redundancy: 1.762 % / Biso Wilson estimate: 22.914 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.099 / Χ2: 1.094 / Net I/σ(I): 6.44 / Num. measured all: 602663
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
1.6-1.71.7290.3781.839473858080548000.7510.52194.4
1.7-1.811.7620.2612.69080654353515440.8650.35894.8
1.81-1.961.8020.1733.938791250756487840.9350.23796.1
1.96-2.151.7430.1145.657815346625448320.9690.15796.2
2.15-2.41.7780.0837.637164242144402830.9830.11495.6
2.4-2.771.7910.0679.476445137183359910.9870.09296.8
2.77-3.391.7240.05211.795125731455297230.9920.07294.5
3.39-4.781.7850.04514.894172224327233740.9930.06396.1
4.78-45.5561.7330.04313.952198213482126830.9940.0694.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→41.064 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 9053 5.02 %
Rwork0.1755 171457 -
obs0.177 180510 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.39 Å2 / Biso mean: 20.0328 Å2 / Biso min: 6.5 Å2
Refinement stepCycle: final / Resolution: 1.6→41.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12286 0 15 2130 14431
Biso mean--10.69 29.15 -
Num. residues----1675
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.61810.27942680.2401562297
1.6181-1.63720.26482890.2279563299
1.6372-1.65710.24562860.2231564899
1.6571-1.67810.25852950.2203567199
1.6781-1.70020.24952670.218575499
1.7002-1.72350.23693000.2079564599
1.7235-1.74810.24423040.2075567099
1.7481-1.77420.23842950.2075566599
1.7742-1.80190.25273050.2142564199
1.8019-1.83150.26762940.2068576299
1.8315-1.86310.23672380.1989568299
1.8631-1.89690.23852870.1944571099
1.8969-1.93340.22482920.1853573899
1.9334-1.97290.21723150.1855569499
1.9729-2.01580.20432890.18175734100
2.0158-2.06270.22962800.185576399
2.0627-2.11430.21933160.18185710100
2.1143-2.17140.20322830.1815722100
2.1714-2.23530.22293570.17315699100
2.2353-2.30740.20243410.1691571199
2.3074-2.38990.21042760.16925715100
2.3899-2.48560.20273150.17045762100
2.4856-2.59870.20383370.17445763100
2.5987-2.73570.21533210.17015726100
2.7357-2.9070.20053070.17325783100
2.907-3.13140.19483330.16715715100
3.1314-3.44640.17782660.1586580699
3.4464-3.94470.16913430.14645740100
3.9447-4.96860.15633340.1402576699
4.9686-41.0640.1993200.1762580898

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