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- PDB-2gbb: Crystal structure of secreted chorismate mutase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 2gbb
TitleCrystal structure of secreted chorismate mutase from Yersinia pestis
Componentsputative chorismate mutase
KeywordsISOMERASE / alpha helical bundle
Function / homology
Function and homology information


salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / periplasmic space
Similarity search - Function
Chorismate mutase, periplasmic / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Chorismate mutase, periplasmic / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / : / Secreted chorismate mutase
Similarity search - Component
Biological speciesYersinia pestis biovar Microtus str. 91001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLadner, J.E. / Reddy, P.T. / Nelson, B.C. / Robinson, H. / Kim, S.-K.
CitationJournal: Febs J. / Year: 2008
Title: A comparative biochemical and structural analysis of the intracellular chorismate mutase (Rv0948c) from Mycobacterium tuberculosis H(37)R(v) and the secreted chorismate mutase (y2828) from Yersinia pestis.
Authors: Kim, S.K. / Reddy, S.K. / Nelson, B.C. / Robinson, H. / Reddy, P.T. / Ladner, J.E.
History
DepositionMar 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 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 1.4Oct 30, 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 / struct_site
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 / _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 chorismate mutase
B: putative chorismate mutase
C: putative chorismate mutase
D: putative chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,87121
Polymers70,8544
Non-polymers2,01717
Water3,477193
1
A: putative chorismate mutase
B: putative chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,58012
Polymers35,4272
Non-polymers1,15310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-97 kcal/mol
Surface area15380 Å2
MethodPISA
2
C: putative chorismate mutase
D: putative chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2929
Polymers35,4272
Non-polymers8657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-70 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.01, 144.09, 116.63
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer. The asymmetric unit contains two dimers.

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Components

#1: Protein
putative chorismate mutase


Mass: 17713.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis biovar Microtus str. 91001 (bacteria)
Species: Yersinia pestis / Strain: KIM / Gene: y2828 / Plasmid: DE3, GroEL:YpCM fusion plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: GenBank: 45435929, UniProt: Q7CHH5*PLUS, chorismate mutase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Well solution: 1.5-1.6 M ammonium sulfate, 0.1 M citrate/phosphate buffer pH 4.2. Protein solution: 5 mg/ml in 0.025 M Tris ph 7.5, 0.0005 M EDTA, 0.0005 M DTT, 0.1 M sodium chloride. Drops: ...Details: Well solution: 1.5-1.6 M ammonium sulfate, 0.1 M citrate/phosphate buffer pH 4.2. Protein solution: 5 mg/ml in 0.025 M Tris ph 7.5, 0.0005 M EDTA, 0.0005 M DTT, 0.1 M sodium chloride. Drops: 1:1 well:protein., VAPOR DIFFUSION, HANGING 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: Nov 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 13 % / Av σ(I) over netI: 8.2 / Number: 566822 / Rmerge(I) obs: 0.113 / Χ2: 1.99 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 43510 / % possible obs: 99.4
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
4.5250459199.90.0825.08913.2
3.594.5244171000.083.45614
3.143.5943751000.0972.61314.3
2.853.1443801000.1271.84714.4
2.652.8543411000.1811.35114.5
2.492.6543391000.231.1314.5
2.372.4943561000.2890.97114.1
2.262.37432199.90.350.90912.4
2.182.26428499.10.420.77310.4
2.12.18410695.30.4690.7178
ReflectionResolution: 2.1→50 Å / Num. obs: 43510 / % possible obs: 99.4 % / Redundancy: 13 % / Rmerge(I) obs: 0.113 / Χ2: 1.991 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
2.1-2.1895.380.46941060.717
2.18-2.2699.110.40.4242840.773
2.26-2.3799.912.40.3543210.909
2.37-2.4910014.10.28943560.971
2.49-2.6510014.50.2343391.13
2.65-2.8510014.50.18143411.351
2.85-3.1410014.40.12743801.847
3.14-3.5910014.30.09743752.613
3.59-4.52100140.0844173.456
4.52-5099.913.20.08245915.089

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se25.6270.8420.8210.6670.891
2Se25.8750.8410.6860.8320.922
3Se24.8950.8120.5860.6460.828
4Se25.3930.8080.9190.8540.893
5Se29.2630.960.8220.620.732
6Se27.5640.9590.6850.880.666
7Se52.1990.6980.8990.9190.943
8Se36.4850.0510.8090.6460.65
9Se59.3790.7110.6060.581.025
10Se55.6170.0570.7030.8560.713
11Se38.9360.6830.6610.5470.655
12Se600.6740.8390.9611.017
13Se47.6110.9820.8760.4990.509
14Se42.1570.9730.6340.0020.426
15Se600.5690.9630.9260.3
16Se600.5630.5430.5760.482
Phasing dmFOM : 0.67 / FOM acentric: 0.68 / FOM centric: 0.57 / Reflection: 22704 / Reflection acentric: 20607 / Reflection centric: 2097
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-29.2790.740.790.591061810251
4.6-7.40.760.790.5931372711426
3.7-4.60.810.830.6838833500383
3.3-3.70.750.760.6338743542332
2.8-3.30.620.630.4867066250456
2.6-2.80.460.470.4240433794249

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.063 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2177 5.1 %RANDOM
Rwork0.207 ---
all0.21 ---
obs-42698 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.383 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---0.13 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 117 193 5233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225112
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9866927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9735618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.06126.008243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47915932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0261524
X-RAY DIFFRACTIONr_chiral_restr0.1760.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023834
X-RAY DIFFRACTIONr_nbd_refined0.2210.22393
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23430
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.214
X-RAY DIFFRACTIONr_mcbond_it1.251.53238
X-RAY DIFFRACTIONr_mcangle_it1.98625031
X-RAY DIFFRACTIONr_scbond_it3.06532141
X-RAY DIFFRACTIONr_scangle_it4.4784.51896
LS refinement shellResolution: 2.1→2.216 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.298 284 -
Rwork0.243 5314 -
obs-5598 89.18 %

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