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- PDB-1szq: Crystal Structure of 2-methylcitrate dehydratase -

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Basic information

Entry
Database: PDB / ID: 1szq
TitleCrystal Structure of 2-methylcitrate dehydratase
Components2-methylcitrate dehydratase
KeywordsSTRUCTURAL GENOMICS / LYASE / Propionate catabolism / 2-methylcitric acid cycle STRUCTURAL GENOMICS TARGET / T819 / NYSGXRC / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


2-methylcitrate dehydratase / 2-methylcitrate dehydratase activity / propionate metabolic process, methylcitrate cycle / aconitate hydratase / aconitate hydratase activity / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding
Similarity search - Function
2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / 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 ...2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / 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 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-methylcitrate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Solorzano, V. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of 2-methylcitrate dehydratase
Authors: Rajashankar, K.R. / Kniewel, R. / Solorzano, V. / Lima, C.D.
History
DepositionApr 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-methylcitrate dehydratase
B: 2-methylcitrate dehydratase


Theoretical massNumber of molelcules
Total (without water)109,1512
Polymers109,1512
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-28 kcal/mol
Surface area34250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.579, 97.579, 219.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsDimer (dimer in the asu is the biological unit)

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Components

#1: Protein 2-methylcitrate dehydratase


Mass: 54575.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B834, DE3 / Gene: PRPD, B0334 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P77243, 2-methylcitrate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 31% PEG4k, 0.1M Tris pH7.75, 0.2M Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 63304 / Num. obs: 63304 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 36.3 Å2 / Rsym value: 0.119 / Net I/σ(I): 11.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 6286 / Rsym value: 0.481 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: Experimental electron density

Resolution: 2.7→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 188358.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: There are two molecules in the asymmetric unit (molecule A and B). Each molecule is comprised of two domains - residues 11-283 and 432-483 form the first domain (Domain A) while residues 284- ...Details: There are two molecules in the asymmetric unit (molecule A and B). Each molecule is comprised of two domains - residues 11-283 and 432-483 form the first domain (Domain A) while residues 284-431 form the second domain (Domain B). Some parts of Domain 2 in molecule B are not very well seen in the electron density map.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2982 4.9 %RANDOM
Rwork0.204 ---
all0.212 60755 --
obs0.204 60755 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9906 Å2 / ksol: 0.353721 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.99 Å211.35 Å20 Å2
2--7.99 Å20 Å2
3----15.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7438 0 0 162 7600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 474 5.3 %
Rwork0.308 8491 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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