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- PDB-3hu5: CRYSTAL STRUCTURE OF isochorismatase family protein from Desulfov... -

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Basic information

Entry
Database: PDB / ID: 3hu5
TitleCRYSTAL STRUCTURE OF isochorismatase family protein from Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough
ComponentsIsochorismatase family protein
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / isochorismatase hydrolase. Desulfovibrio vulgaris / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homologyIsochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / catalytic activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Isochorismatase family protein
Function and homology information
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF isochorismatase family protein from Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJun 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isochorismatase family protein
B: Isochorismatase family protein


Theoretical massNumber of molelcules
Total (without water)44,0862
Polymers44,0862
Non-polymers00
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Isochorismatase family protein

A: Isochorismatase family protein

B: Isochorismatase family protein

B: Isochorismatase family protein


Theoretical massNumber of molelcules
Total (without water)88,1724
Polymers88,1724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
Buried area8280 Å2
ΔGint-12 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.663, 116.790, 105.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsbiological unit is the same as asymmetric unit.

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Components

#1: Protein Isochorismatase family protein


Mass: 22043.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / Gene: DVU_0033 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q72G28
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3 % / Av σ(I) over netI: 23.32 / Number: 356345 / Rmerge(I) obs: 0.084 / Χ2: 2.42 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 119171 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.075098.110.0596.5973.1
3.234.0799.510.0616.3112.9
2.823.2399.710.0725.3973
2.562.8299.710.0834.4993.1
2.382.5699.810.0833.493.1
2.242.3899.910.0893.0413.1
2.132.2410010.0982.4333.1
2.042.1399.910.1082.1033.1
1.962.0410010.1271.7133.1
1.891.9610010.1511.4283.1
1.831.8910010.1841.2833.1
1.781.8310010.231.1563.1
1.731.7810010.2561.1243.1
1.691.7310010.3131.0183.1
1.651.6999.910.3660.9783
1.621.6598.210.4010.942.9
1.581.629510.4340.9412.8
1.551.5891.110.4560.9432.8
1.531.5585.710.480.8932.7
1.51.5380.210.5690.8832.6
ReflectionResolution: 1.5→50 Å / Num. obs: 119171 / % possible obs: 97.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.084 / Χ2: 2.423 / Net I/σ(I): 23.318
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.532.60.56948960.883180.2
1.53-1.552.70.4852620.893185.7
1.55-1.582.80.45655750.943191.1
1.58-1.622.80.43457690.941195
1.62-1.652.90.40160470.94198.2
1.65-1.6930.36660990.978199.9
1.69-1.733.10.31361171.0181100
1.73-1.783.10.25661111.1241100
1.78-1.833.10.2361221.1561100
1.83-1.893.10.18461131.2831100
1.89-1.963.10.15161711.4281100
1.96-2.043.10.12760781.7131100
2.04-2.133.10.10861552.103199.9
2.13-2.243.10.09861082.4331100
2.24-2.383.10.08961333.041199.9
2.38-2.563.10.08361073.49199.8
2.56-2.823.10.08360754.499199.7
2.82-3.2330.07261035.397199.7
3.23-4.072.90.06160896.311199.5
4.07-503.10.05960416.597198.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→30.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.843 / SU B: 3.825 / SU ML: 0.062 / SU R Cruickshank DPI: 0.077 / SU Rfree: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3024 5.1 %RANDOM
Rwork0.187 ---
obs0.189 59514 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.08 Å2 / Biso mean: 19.482 Å2 / Biso min: 5.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 0 424 3196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222810
X-RAY DIFFRACTIONr_angle_refined_deg2.3371.9723820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9735378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56123.148108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3615446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.971526
X-RAY DIFFRACTIONr_chiral_restr0.1390.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212104
X-RAY DIFFRACTIONr_mcbond_it1.4061.51876
X-RAY DIFFRACTIONr_mcangle_it2.19823000
X-RAY DIFFRACTIONr_scbond_it3.6393934
X-RAY DIFFRACTIONr_scangle_it5.1714.5820
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 198 -
Rwork0.294 3332 -
all-3530 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3822-0.0267-0.18110.60040.01760.23670.0141-0.0136-0.00110.1374-0.01180.0401-0.00460.0467-0.00240.0329-0.00340.00850.0468-0.00240.003929.020249.164339.5729
20.3616-0.4673-0.14970.78580.26180.1793-0.1537-0.0422-0.07750.1660.05780.01950.04470.03640.09590.08550.02790.05050.02610.0370.14179.031678.093236.0801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 195
2X-RAY DIFFRACTION1A205 - 502
3X-RAY DIFFRACTION2B6 - 195
4X-RAY DIFFRACTION2B205 - 499

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