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- PDB-2rd1: X-Ray structure of the protein Q7CQI7. Northeast Structural Genom... -

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Basic information

Entry
Database: PDB / ID: 2rd1
TitleX-Ray structure of the protein Q7CQI7. Northeast Structural Genomics Consortium target StR87A
ComponentsPutative outer membrane lipoprotein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / Q7CQI7 / StR87A / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Lipoprotein
Function / homology
Function and homology information


Protein of unknown function DUF903 / : / Bacterial protein of unknown function (DUF903) / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Outer membrane lipoprotein
Similarity search - Component
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, D. / Fang, Y. / Owens, L. / Mao, L.-C. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, D. / Fang, Y. / Owens, L. / Mao, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of the protein Q7CQI7.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wan, D. / Fang, Y. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 16, 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: Putative outer membrane lipoprotein
B: Putative outer membrane lipoprotein
C: Putative outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)21,4513
Polymers21,4513
Non-polymers00
Water84747
1
A: Putative outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,1501
Polymers7,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,1501
Polymers7,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,1501
Polymers7,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Putative outer membrane lipoprotein

C: Putative outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)14,3012
Polymers14,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1930 Å2
MethodPISA
5
B: Putative outer membrane lipoprotein

B: Putative outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)14,3012
Polymers14,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.696, 57.696, 100.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative outer membrane lipoprotein


Mass: 7150.480 Da / Num. of mol.: 3 / Fragment: Residues 20-73
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Species: Salmonella typhimurium / Strain: LT2, SGSC1412 / Gene: STM1585 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CQI7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.95 Å3/Da / Density % sol: 36.85 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 18% PEG 4000, 0.1M Ammonium chloride, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14487 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 34.8 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 25.6
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 7.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.99 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 127079.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing. Bulk solvent model was used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.264 658 5 %RANDOM
Rwork0.207 ---
obs0.207 7959 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.6913 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2--1.76 Å20 Å2
3----3.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 48 1409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 101 5.2 %
Rwork0.227 1859 -
obs--82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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