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- PDB-2iqi: Crystal structure of protein XCC0632 from Xanthomonas campestris,... -

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Basic information

Entry
Database: PDB / ID: 2iqi
TitleCrystal structure of protein XCC0632 from Xanthomonas campestris, Pfam DUF330
ComponentsHypothetical protein XCC0632
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyABC-type transport auxiliary lipoprotein component / ABC-type transport auxiliary lipoprotein component / ABC-type transport auxiliary lipoprotein component / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ABC_trans_aux domain-containing protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsBonanno, J.B. / Gilmore, J. / Bain, K.T. / Mckenzie, C. / Pelletier, L. / Wasserman, S. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein XCC0632 from Xanthomonas campestris pv. campestris
Authors: Bonanno, J.B. / Gilmore, J. / Bain, K.T. / Mckenzie, C. / Pelletier, L. / Wasserman, S. / Burley, S.K. / Almo, S.C.
History
DepositionOct 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: 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.name
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
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein XCC0632
B: Hypothetical protein XCC0632
C: Hypothetical protein XCC0632
D: Hypothetical protein XCC0632
E: Hypothetical protein XCC0632
F: Hypothetical protein XCC0632
G: Hypothetical protein XCC0632
H: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)164,8018
Polymers164,8018
Non-polymers00
Water3,657203
1
A: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)20,6001
Polymers20,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)20,6001
Polymers20,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)20,6001
Polymers20,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)20,6001
Polymers20,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)20,6001
Polymers20,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)20,6001
Polymers20,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)20,6001
Polymers20,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Hypothetical protein XCC0632


Theoretical massNumber of molelcules
Total (without water)20,6001
Polymers20,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.933, 103.114, 121.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsprobable monomer

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Components

#1: Protein
Hypothetical protein XCC0632


Mass: 20600.158 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: pv. campestris / Gene: XCC0632 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PCT0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Hepes, pH 7.5, 20% PEG 4000, 10% isopropanol, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 24, 2006
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.7→19.937 Å / Num. all: 54597 / Num. obs: 54433 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 14.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 3 / Num. measured all: 56036 / Num. unique all: 7844 / Rsym value: 0.697 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.89 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.649 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.586 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1548 2.8 %RANDOM
Rwork0.209 ---
obs0.211 54389 99.97 %-
all-54405 --
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 mean: 46.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10477 0 0 203 10680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210693
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.94414640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10551359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65823.541449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.223151627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8461589
X-RAY DIFFRACTIONr_chiral_restr0.0990.21739
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028121
X-RAY DIFFRACTIONr_nbd_refined0.2180.24181
X-RAY DIFFRACTIONr_nbtor_refined0.3130.27209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2435
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.27
X-RAY DIFFRACTIONr_mcbond_it0.8211.57060
X-RAY DIFFRACTIONr_mcangle_it1.395211170
X-RAY DIFFRACTIONr_scbond_it2.2134177
X-RAY DIFFRACTIONr_scangle_it3.6664.53470
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 106 -
Rwork0.253 3775 -
obs-3881 99.79 %

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