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- PDB-2qyz: Crystal structure of the uncharacterized protein CTC02137 from Cl... -

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Basic information

Entry
Database: PDB / ID: 2qyz
TitleCrystal structure of the uncharacterized protein CTC02137 from Clostridium tetani E88
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Clostridium tetani E88 / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


ctc02137 like domains / YopX-like domains / Conserved hypothetical protein CHP1671 / YopX-like, C-terminal / YopX protein / YopX protein / Dna Ligase; domain 1 / SH3 type barrels. / Roll / 2-Layer Sandwich ...ctc02137 like domains / YopX-like domains / Conserved hypothetical protein CHP1671 / YopX-like, C-terminal / YopX protein / YopX protein / Dna Ligase; domain 1 / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
YopX domain-containing protein
Similarity search - Component
Biological speciesClostridium tetani E88 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.04 Å
AuthorsMalashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Wasserman, T. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the uncharacterized protein CTC02137 from Clostridium tetani E88.
Authors: Malashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Wasserman, T. / Burley, S.K. / Almo, S.C.
History
DepositionAug 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. THE DIMER IS DISULFIDE-LINKED THROUGH CYS-92.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,3841
Polymers16,3841
Non-polymers00
Water1,20767
1
A: Uncharacterized protein

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,7692
Polymers32,7692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area4150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.711, 40.711, 156.753
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Detailsdisulfide linked dimer is formed around the crystallographic two-fold axis. Asymmetric unit contains one subunit.

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Components

#1: Protein Uncharacterized protein


Mass: 16384.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetani E88 (bacteria) / Species: Clostridium tetani / Strain: E88, Massachusetts / Gene: CTC_02137 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q892G2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.5
Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, temperature 294K

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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: Jul 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 18.3 / Number: 81550 / Rmerge(I) obs: 0.035 / Χ2: 1.14 / D res high: 2.04 Å / D res low: 50 Å / Num. obs: 16582 / % possible obs: 89.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.395096.310.0241.7845.3
3.494.3996.610.0362.0885.3
3.053.4910010.0361.2445.7
2.773.0510010.0480.9925.7
2.572.7799.910.0630.8095.7
2.422.5710010.090.6815.5
2.32.4298.910.1090.6184.7
2.22.389.310.1961.3693.5
2.112.271.610.1720.5233
2.042.1139.610.1830.5092.6
ReflectionResolution: 2.04→50 Å / Num. obs: 16582 / % possible obs: 89.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.035 / Χ2: 1.143 / Net I/σ(I): 18.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.04-2.112.60.1837220.509139.6
2.11-2.230.17213260.523171.6
2.2-2.33.50.19616561.369189.3
2.3-2.424.70.10918470.618198.9
2.42-2.575.50.0918660.6811100
2.57-2.775.70.06318340.809199.9
2.77-3.055.70.04818480.9921100
3.05-3.495.70.03618721.2441100
3.49-4.395.30.03617962.088196.6
4.39-505.30.02418151.784196.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
SHELXSphasing
RefinementResolution: 2.04→19.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.938 / SU B: 22.616 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Bijvoet differences were used for phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 435 4.8 %RANDOM
Rwork0.191 ---
obs0.194 9007 92.09 %-
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: 54.382 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.04→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 0 67 1111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221066
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.9561438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5385128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.19525.61457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26815202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.263155
X-RAY DIFFRACTIONr_chiral_restr0.1320.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02809
X-RAY DIFFRACTIONr_nbd_refined0.2430.2412
X-RAY DIFFRACTIONr_nbtor_refined0.3220.2718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.29
X-RAY DIFFRACTIONr_mcbond_it1.8071.5657
X-RAY DIFFRACTIONr_mcangle_it5.987201031
X-RAY DIFFRACTIONr_scbond_it11.64520476
X-RAY DIFFRACTIONr_scangle_it5.2134.5406
LS refinement shellResolution: 2.04→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.532 21 -
Rwork0.326 291 -
all-312 -
obs--45.55 %
Refinement TLS params.Method: refined / Origin x: 0.9503 Å / Origin y: 5.2605 Å / Origin z: 36.9146 Å
111213212223313233
T-0.0044 Å2-0.1084 Å20.0072 Å2--0.1403 Å2-0.0111 Å2---0.0676 Å2
L1.3446 °2-0.138 °2-0.4823 °2-1.9553 °2-1.3127 °2--4.7512 °2
S0.0854 Å °-0.2281 Å °0.0447 Å °0.1964 Å °-0.2359 Å °0.0842 Å °0.0135 Å °0.1044 Å °0.1505 Å °

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