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- PDB-3q9d: Crystal Structure of Cpn0803 from C. pneumoniae. -

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Basic information

Entry
Database: PDB / ID: 3q9d
TitleCrystal Structure of Cpn0803 from C. pneumoniae.
ComponentsProtein CPn_0803/CP_1068/CPj0803/CpB0832
KeywordsUNKNOWN FUNCTION / Coiled-coil / Needle Tip TypeIII Secretion System
Function / homology
Function and homology information


Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1050 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1130 / CT_584-like / CT_584-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein CPn_0803/CP_1068/CPj0803/CpB0832
Similarity search - Component
Biological speciesChlamydophila pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsStone, C.B. / Sugiman-Marangos, S.N. / Junop, M.S. / Mahony, J.B.
CitationJournal: To be Published
Title: Crystal Structure of Cpn0803 from C. pneumoniae.
Authors: Stone, C.B. / Sugiman-Marangos, S.N. / Junop, M.S. / Mahony, J.B.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CPn_0803/CP_1068/CPj0803/CpB0832
B: Protein CPn_0803/CP_1068/CPj0803/CpB0832


Theoretical massNumber of molelcules
Total (without water)51,2372
Polymers51,2372
Non-polymers00
Water4,414245
1
A: Protein CPn_0803/CP_1068/CPj0803/CpB0832
B: Protein CPn_0803/CP_1068/CPj0803/CpB0832

A: Protein CPn_0803/CP_1068/CPj0803/CpB0832
B: Protein CPn_0803/CP_1068/CPj0803/CpB0832

A: Protein CPn_0803/CP_1068/CPj0803/CpB0832
B: Protein CPn_0803/CP_1068/CPj0803/CpB0832


Theoretical massNumber of molelcules
Total (without water)153,7106
Polymers153,7106
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area27250 Å2
ΔGint-244 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.392, 86.392, 99.591
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

21A-236-

HOH

31B-207-

HOH

41B-292-

HOH

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Components

#1: Protein Protein CPn_0803/CP_1068/CPj0803/CpB0832


Mass: 25618.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydophila pneumoniae (bacteria) / Gene: CPn_0803, CP_1068, CPj0803, CpB0832 / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z7A3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 298 K / pH: 7
Details: 0.2M potassium nitrate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X29A10.979
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 25, 2010
ADSC QUANTUM 3152CCDJun 23, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSADMx-ray1
2SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.11
ReflectionResolution: 2→50 Å / Num. obs: 28547 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 2.09
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine: dev_597)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→43.196 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 1416 5.11 %
Rwork0.1758 --
obs0.1774 27704 97.13 %
all-27704 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3308 Å2-0 Å2-0 Å2
2--1.3308 Å20 Å2
3----0.8908 Å2
Refinement stepCycle: LAST / Resolution: 2→43.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 0 245 3089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093030
X-RAY DIFFRACTIONf_angle_d1.2334117
X-RAY DIFFRACTIONf_dihedral_angle_d15.5691184
X-RAY DIFFRACTIONf_chiral_restr0.077471
X-RAY DIFFRACTIONf_plane_restr0.006545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07130.22141540.18082396X-RAY DIFFRACTION90
2.0713-2.15430.21371380.16472521X-RAY DIFFRACTION93
2.1543-2.25230.21991290.17182588X-RAY DIFFRACTION96
2.2523-2.3710.23261370.17172626X-RAY DIFFRACTION97
2.371-2.51960.2431480.18322638X-RAY DIFFRACTION98
2.5196-2.71410.19151470.18522658X-RAY DIFFRACTION98
2.7141-2.98710.22491490.18372673X-RAY DIFFRACTION99
2.9871-3.41920.23221280.19262710X-RAY DIFFRACTION100
3.4192-4.30730.18841620.16012708X-RAY DIFFRACTION100
4.3073-43.20610.18621240.17392770X-RAY DIFFRACTION99

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