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- PDB-2a67: Crystal structure of Isochorismatase family protein -

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Basic information

Entry
Database: PDB / ID: 2a67
TitleCrystal structure of Isochorismatase family protein
Componentsisochorismatase family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isochorismatase family protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChang, C. / Hatzos, C. / Collart, F. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Isochorismatase family protein
Authors: Chang, C. / Hatzos, C. / Collart, F. / Moy, S. / Joachimiak, A.
History
DepositionJul 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: isochorismatase family protein
B: isochorismatase family protein
C: isochorismatase family protein
D: isochorismatase family protein


Theoretical massNumber of molelcules
Total (without water)76,9264
Polymers76,9264
Non-polymers00
Water6,053336
1
A: isochorismatase family protein
D: isochorismatase family protein


Theoretical massNumber of molelcules
Total (without water)38,4632
Polymers38,4632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-10 kcal/mol
Surface area15170 Å2
MethodPISA
2
B: isochorismatase family protein
C: isochorismatase family protein


Theoretical massNumber of molelcules
Total (without water)38,4632
Polymers38,4632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-11 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.972, 102.601, 91.088
Angle α, β, γ (deg.)90.00, 116.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-172-

HOH

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Components

#1: Protein
isochorismatase family protein


Mass: 19231.400 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZG7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.2 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: PEG1000, Na/K Phosphate, NaCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 13, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 63727 / Num. obs: 62962 / % possible obs: 98.8 % / Observed criterion σ(I): -5 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.61 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.863 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 3196 5.1 %RANDOM
Rwork0.18978 ---
all0.19193 63365 --
obs0.19193 62953 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.773 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.02 Å2
2---0.23 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5367 0 0 336 5703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225565
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9327584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9725682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60724.591281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10915937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2851528
X-RAY DIFFRACTIONr_chiral_restr0.1650.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024256
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.22616
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23722
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2348
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4340.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1441.53495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78425476
X-RAY DIFFRACTIONr_scbond_it3.09132347
X-RAY DIFFRACTIONr_scangle_it3.9834.52101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 194 -
Rwork0.225 4139 -
obs--93.32 %

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