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- PDB-6s62: Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseu... -

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Basic information

Entry
Database: PDB / ID: 6s62
TitleCrystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form.
ComponentsPropionate catabolic protein PrpD
KeywordsISOMERASE / 2-methlycitrate dehydratase / MmgE/PrpD / propionate metabolism
Function / homology
Function and homology information


2-methylcitrate dehydratase / 2-methylcitrate dehydratase activity / propionate metabolic process, methylcitrate cycle / 2 iron, 2 sulfur cluster binding
Similarity search - Function
2-methylcitrate dehydratase PrpD / MmgE/PrpD / MmgE/PrpD superfamily / MmgE/PrpD superfamily, domain 1 / MmgE/PrpD superfamily, domain 2 / MmgE/PrpD, N-terminal / MmgE/PrpD, C-terminal / MmgE/PrpD N-terminal domain / MmgE/PrpD C-terminal domain
Similarity search - Domain/homology
2-methylcitrate dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsWijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M019411/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/R005435/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form.
Authors: Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Propionate catabolic protein PrpD
B: Propionate catabolic protein PrpD
C: Propionate catabolic protein PrpD
D: Propionate catabolic protein PrpD
E: Propionate catabolic protein PrpD
F: Propionate catabolic protein PrpD


Theoretical massNumber of molelcules
Total (without water)329,7226
Polymers329,7226
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23990 Å2
ΔGint-96 kcal/mol
Surface area97330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.480, 124.540, 126.850
Angle α, β, γ (deg.)90.000, 116.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Propionate catabolic protein PrpD


Mass: 54953.602 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: prpD, PA0792
Variant: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I5E6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS.HCl pH 8.5, 15-25 %(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.36→113.25 Å / Num. obs: 140797 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.72 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.074 / Rrim(I) all: 0.146 / Net I/σ(I): 7.2 / Num. measured all: 518784 / Scaling rejects: 590
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.36-2.420.93535641103880.610.5621.0951.899.9
10.55-113.250.055567616480.9930.0330.06514.999.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SZQ

1szq


Resolution: 2.36→113.175 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.52
RfactorNum. reflection% reflection
Rfree0.2599 7169 5.12 %
Rwork0.2061 --
obs0.2089 140126 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 201.18 Å2 / Biso mean: 34.2104 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 2.36→113.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22733 0 0 193 22926
Biso mean---24.03 -
Num. residues----2906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823247
X-RAY DIFFRACTIONf_angle_d0.96131548
X-RAY DIFFRACTIONf_chiral_restr0.0533498
X-RAY DIFFRACTIONf_plane_restr0.0064140
X-RAY DIFFRACTIONf_dihedral_angle_d13.92614009
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.36-2.38420.33452190.2824421094
2.3842-2.41220.37312060.2825441899
2.4122-2.44170.34942110.2675444999
2.4417-2.47260.3162170.261444099
2.4726-2.50510.34532280.2569440299
2.5051-2.53940.33472460.25274462100
2.5394-2.57570.3432380.25754417100
2.5757-2.61420.32692370.26734408100
2.6142-2.6550.38532290.2936439999
2.655-2.69850.36492150.2793439498
2.6985-2.74510.35812220.2473441699
2.7451-2.7950.28962400.2372440199
2.795-2.84880.31772780.22554404100
2.8488-2.90690.27572620.2249442799
2.9069-2.97010.29192870.22034393100
2.9701-3.03920.27972570.22454383100
3.0392-3.11520.29232060.22624504100
3.1152-3.19950.26482490.22744438100
3.1995-3.29360.25972530.21484436100
3.2936-3.39990.25422800.21254368100
3.3999-3.52150.26342260.219448999
3.5215-3.66250.24632260.20284440100
3.6625-3.82910.25422210.19574466100
3.8291-4.0310.23062460.1929443999
4.031-4.28360.21132660.16354446100
4.2836-4.61430.21822570.15424479100
4.6143-5.07870.20352620.15424444100
5.0787-5.81360.22062220.17124497100
5.8136-7.32430.20412180.1699452799
7.3243-113.1750.15172450.1367456199

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