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- PDB-4maq: Crystal Structure of a putative fumarylpyruvate hydrolase from Bu... -

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Basic information

Entry
Database: PDB / ID: 4maq
TitleCrystal Structure of a putative fumarylpyruvate hydrolase from Burkholderia cenocepacia
ComponentsPutative fumarylpyruvate hydrolase
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


ureidoglycolate lyase activity / acetylpyruvate hydrolase activity / urate catabolic process / metal ion binding
Similarity search - Function
Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Fumarylpyruvate hydrolase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of a putative fumarylpyruvate hydrolase from Burkholderia cenocepacia
Authors: Dranow, D.M. / Lukacs, C.M. / Edwards, T.E. / Lorimer, D.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative fumarylpyruvate hydrolase
B: Putative fumarylpyruvate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6784
Polymers51,5542
Non-polymers1242
Water13,872770
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-10 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.170, 51.630, 186.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Putative fumarylpyruvate hydrolase


Mass: 25776.949 Da / Num. of mol.: 2 / Fragment: BuceA.00471.a
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BceJ2315_51410, BCAM1692 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EKU2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+(h8): 25% PEG-3350, 0.1M BisTris/HCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 98388 / Num. obs: 97601 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 19.735 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4-1.440.4782.8334431714199.9
1.44-1.480.3773.6133860701099.9
1.48-1.520.34.6433146682399.9
1.52-1.570.2535.5331904658499.7
1.57-1.620.2047.0431196641699.8
1.62-1.670.178.429758617599.5
1.67-1.740.18510.1228803596299.6
1.74-1.810.17312.6627338571099.4
1.81-1.890.14415.7325997548399.2
1.89-1.980.11618.9923976522399.1
1.98-2.090.09921.7822537495698.6
2.09-2.210.08823.7820887467698.5
2.21-2.370.08125.4219644441498.7
2.37-2.560.07526.8818720414298.8
2.56-2.80.0672917442384099
2.8-3.130.06131.2316085350299.1
3.13-3.610.05433.1914444310099.1
3.61-4.430.04534.8912502266098.8
4.43-6.260.03735.659891209898.1
6.260.0333.965083115792.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.85 Å
Translation2.5 Å44.85 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NR9

1nr9


Resolution: 1.4→19.85 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1708 / WRfactor Rwork: 0.1339 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.926 / SU B: 1.633 / SU ML: 0.03 / SU R Cruickshank DPI: 0.0527 / SU Rfree: 0.0513 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1678 4873 5 %RANDOM
Rwork0.1321 ---
all0.134 97494 --
obs0.134 92621 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.38 Å2 / Biso mean: 16.7592 Å2 / Biso min: 5.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.06 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 8 770 4156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193578
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9414913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9185478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95222.384151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.41815491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5051531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212827
X-RAY DIFFRACTIONr_mcbond_it1.6341.211851
X-RAY DIFFRACTIONr_mcangle_it2.2061.8212316
X-RAY DIFFRACTIONr_scbond_it2.0221.4051727
X-RAY DIFFRACTIONr_rigid_bond_restr1.93433578
X-RAY DIFFRACTIONr_sphericity_free39.5285131
X-RAY DIFFRACTIONr_sphericity_bonded13.12354111
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 272 -
Rwork0.225 6823 -
all-7095 -
obs--99.92 %

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