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- PDB-3ocj: The crystal structure of a possilbe exported protein from Bordete... -

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Basic information

Entry
Database: PDB / ID: 3ocj
TitleThe crystal structure of a possilbe exported protein from Bordetella parapertussis
ComponentsPutative exported protein
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Methyltransferase domain / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Exported protein
Similarity search - Component
Biological speciesBordetella parapertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsTan, K. / Bigelow, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possilbe exported protein from Bordetella parapertussis
Authors: Tan, K. / Bigelow, L. / Buck, K. / Joachimiak, A.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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_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_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

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Assembly

Deposited unit
A: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7224
Polymers34,2811
Non-polymers4413
Water7,224401
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.233, 49.312, 145.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-627-

HOH

DetailsExperimentally unknown. It is predicted to be a monomer.

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Components

#1: Protein Putative exported protein


Mass: 34281.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis (bacteria) / Gene: BPP1064 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q7WBE0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M imidazole, 1.0M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 6, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.39→25 Å / Num. all: 69592 / Num. obs: 69592 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 33.6
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.53 / Num. unique all: 3408 / % possible all: 97.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.39→24.656 Å / SU ML: 0.18 / σ(F): 0.04 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3268 5.05 %random
Rwork0.1873 ---
all0.1885 64679 --
obs0.1885 64679 91.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.671 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1311 Å20 Å2-0 Å2
2--0.0545 Å20 Å2
3----3.1856 Å2
Refinement stepCycle: LAST / Resolution: 1.39→24.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 30 401 2799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062514
X-RAY DIFFRACTIONf_angle_d1.0923423
X-RAY DIFFRACTIONf_dihedral_angle_d17.335944
X-RAY DIFFRACTIONf_chiral_restr0.073369
X-RAY DIFFRACTIONf_plane_restr0.005455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3896-1.43920.30332870.27275234X-RAY DIFFRACTION79
1.4392-1.49690.25253000.22415717X-RAY DIFFRACTION86
1.4969-1.5650.24223080.20055870X-RAY DIFFRACTION89
1.565-1.64750.2213460.17756096X-RAY DIFFRACTION92
1.6475-1.75060.1923530.17126166X-RAY DIFFRACTION93
1.7506-1.88580.19053220.17396331X-RAY DIFFRACTION95
1.8858-2.07550.20643580.17256465X-RAY DIFFRACTION97
2.0755-2.37560.19143220.16356665X-RAY DIFFRACTION99
2.3756-2.99210.20123530.18066728X-RAY DIFFRACTION99
2.9921-24.65990.20733190.19036139X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 21.6357 Å / Origin y: 20.8609 Å / Origin z: 18.4435 Å
111213212223313233
T0.093 Å2-0.0005 Å2-0.0031 Å2-0.0995 Å20.0012 Å2--0.1087 Å2
L0.427 °2-0.0707 °2-0.0804 °2-0.3808 °20.0635 °2--1.1215 °2
S0.008 Å °-0.0132 Å °-0.0168 Å °0.0234 Å °0.0072 Å °0.0251 Å °0.058 Å °-0.0822 Å °-0.0117 Å °
Refinement TLS groupSelection details: chain A

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