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- PDB-3ocm: The crystal structure of a domain from a possible membrane protei... -

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Basic information

Entry
Database: PDB / ID: 3ocm
TitleThe crystal structure of a domain from a possible membrane protein of Bordetella parapertussis
ComponentsPutative membrane protein
KeywordsMEMBRANE PROTEIN / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


flavin adenine dinucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
Integral membrane protein TerC / Integral membrane protein TerC family / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily ...Integral membrane protein TerC / Integral membrane protein TerC family / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain superfamily / CBS domain / CBS domain / Roll / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Membrane protein
Similarity search - Component
Biological speciesBordetella parapertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsTan, K. / Tesar, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain from a possible membrane protein of Bordetella parapertussis
Authors: Tan, K. / Tesar, C. / Cobb, G. / 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 1.2Nov 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Putative membrane protein
B: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,81318
Polymers38,1162
Non-polymers1,69716
Water5,729318
1
A: Putative membrane protein
B: Putative membrane protein
hetero molecules

A: Putative membrane protein
B: Putative membrane protein
hetero molecules

A: Putative membrane protein
B: Putative membrane protein
hetero molecules

A: Putative membrane protein
B: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,25172
Polymers152,4638
Non-polymers6,78864
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area33320 Å2
ΔGint-686 kcal/mol
Surface area50220 Å2
MethodPISA
2
A: Putative membrane protein
B: Putative membrane protein
hetero molecules

A: Putative membrane protein
B: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,62536
Polymers76,2314
Non-polymers3,39432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area15880 Å2
ΔGint-329 kcal/mol
Surface area25890 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-159 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.289, 152.289, 46.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsExperimentally unknown. It is possibly a dimer.

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Components

#1: Protein Putative membrane protein


Mass: 19057.865 Da / Num. of mol.: 2 / Fragment: residues 299-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis (bacteria) / Gene: BPP2278 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q7W867
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 1.8M MgSO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.8→39 Å / Num. all: 51470 / Num. obs: 51470 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 28
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2508 / % possible all: 99.6

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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: 1.801→38.62 Å / SU ML: 0.16 / σ(F): 0.03 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 2491 5.07 %random
Rwork0.1729 ---
all0.1742 49105 --
obs0.1742 49105 95.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.806 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6067 Å20 Å2-0 Å2
2--2.6067 Å20 Å2
3----5.2133 Å2
Refinement stepCycle: LAST / Resolution: 1.801→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 96 318 2696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082449
X-RAY DIFFRACTIONf_angle_d1.2663344
X-RAY DIFFRACTIONf_dihedral_angle_d17.282933
X-RAY DIFFRACTIONf_chiral_restr0.074389
X-RAY DIFFRACTIONf_plane_restr0.005429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.86540.25172160.22714015X-RAY DIFFRACTION83
1.8654-1.940.21422280.19464250X-RAY DIFFRACTION88
1.94-2.02830.20362380.17954439X-RAY DIFFRACTION92
2.0283-2.13530.19142520.16624592X-RAY DIFFRACTION95
2.1353-2.2690.20212280.16144690X-RAY DIFFRACTION97
2.269-2.44420.19532610.16624769X-RAY DIFFRACTION98
2.4442-2.69010.20942830.1794802X-RAY DIFFRACTION99
2.6901-3.07920.2082530.17774896X-RAY DIFFRACTION99
3.0792-3.87890.18472630.16054971X-RAY DIFFRACTION100
3.8789-38.62920.18292690.16975190X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9915-0.2055-0.10150.56280.19280.54230.05380.1087-0.0062-0.0838-0.02640.02440.07760.0725-0.01910.11730.03470.00390.11220.01410.080126.066765.245614.5323
20.4217-0.32870.45061.0304-0.13250.8176-0.055-0.09870.04590.08220.0715-0.0516-0.02290.0713-0.00780.12960.04460.00380.1640.00590.114231.412871.512832.6308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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