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- PDB-3oco: The crystal structure of a Hemolysin-like protein containing CBS ... -

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Basic information

Entry
Database: PDB / ID: 3oco
TitleThe crystal structure of a Hemolysin-like protein containing CBS domain of Oenococcus oeni PSU
ComponentsHemolysin-like protein containing CBS domains
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


flavin adenine dinucleotide binding / plasma membrane
Similarity search - Function
: / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS-domain / CBS-domain ...: / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Hemolysin-like protein containing CBS domains
Similarity search - Component
Biological speciesOenococcus oeni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.204 Å
AuthorsTan, K. / Hatzos, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a Hemolysin-like protein containing CBS domain of Oenococcus oeni PSU
Authors: Tan, K. / Hatzos, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin-like protein containing CBS domains
B: Hemolysin-like protein containing CBS domains


Theoretical massNumber of molelcules
Total (without water)35,7172
Polymers35,7172
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-22 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.454, 93.556, 92.061
Angle α, β, γ (deg.)90.00, 102.93, 90.00
Int Tables number5
Space group name H-MC121
DetailsExperimentally unknown. It is predicted to be a dimer.

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Components

#1: Protein Hemolysin-like protein containing CBS domains


Mass: 17858.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oenococcus oeni (bacteria) / Strain: PSU-1 / Gene: OEOE_0137 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q04HE1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2M LiCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924, 0.97943
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979431
ReflectionResolution: 2.2→34 Å / Num. all: 17816 / Num. obs: 17816 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.2 / Num. unique all: 715 / % possible all: 77.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.204→33.591 Å / SU ML: 0.3 / σ(F): 0.04 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 845 5.24 %random
Rwork0.1963 ---
all0.1995 16140 --
obs0.1995 16140 86.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.612 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.7091 Å2-0 Å2-1.8489 Å2
2---16.3982 Å2-0 Å2
3---1.6891 Å2
Refinement stepCycle: LAST / Resolution: 2.204→33.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 0 111 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092194
X-RAY DIFFRACTIONf_angle_d1.2242970
X-RAY DIFFRACTIONf_dihedral_angle_d18.785820
X-RAY DIFFRACTIONf_chiral_restr0.08342
X-RAY DIFFRACTIONf_plane_restr0.004388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2035-2.34150.33121000.26561915X-RAY DIFFRACTION65
2.3415-2.52230.35421180.25032320X-RAY DIFFRACTION80
2.5223-2.7760.32041420.23522516X-RAY DIFFRACTION86
2.776-3.17740.2871480.21352693X-RAY DIFFRACTION91
3.1774-4.00210.25511670.18132902X-RAY DIFFRACTION99
4.0021-33.59450.1981700.15472949X-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)
10.5159-0.3548-0.2112.0123-0.28410.36330.23690.07470.0462-0.5818-0.2399-0.0783-0.1203-0.05110.03830.26050.11210.01450.1405-0.01210.0875-0.477588.464626.1431
20.5007-0.35690.44312.19560.03420.70960.2210.0768-0.0683-0.6533-0.34820.13480.11740.06890.11980.25070.1348-0.01130.11030.00440.06652.350965.593726.1569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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