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- PDB-3bee: Crystal structure of putative YfrE protein from Vibrio parahaemol... -

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Basic information

Entry
Database: PDB / ID: 3bee
TitleCrystal structure of putative YfrE protein from Vibrio parahaemolyticus
ComponentsPutative YfrE protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putaive YfrE protein / Vibrio parahaemolyticus / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / TPR repeat
Function / homology
Function and homology information


cytochrome complex assembly / membrane
Similarity search - Function
: / Cytochrome c-type biogenesis protein H TPR domain / : / Tetratricopeptide repeat domain / TPR repeat profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Putaive YfrE protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsChang, C. / Hatzos, C. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative YfrE protein from Vibrio parahaemolyticus.
Authors: Chang, C. / Hatzos, C. / Abdullah, J. / Joachimiak, A.
History
DepositionNov 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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 YfrE protein
B: Putative YfrE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3866
Polymers21,1372
Non-polymers2484
Water1,856103
1
A: Putative YfrE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7554
Polymers10,5691
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative YfrE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6312
Polymers10,5691
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.383, 82.383, 74.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative YfrE protein


Mass: 10568.690 Da / Num. of mol.: 2 / Fragment: Residues 146-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VP1931 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q87ND7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.4 M Ammonium sulfate, 0.1 M Bicine, pH 9.0, 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: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 14481 / Num. obs: 14459 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 55.96
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 7.11 / Num. unique all: 1411 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→41.2 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.786 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21447 726 5 %RANDOM
Rwork0.19093 ---
all0.1921 14417 --
obs0.1921 14417 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.329 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 16 103 1566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221498
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9732031
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5895185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52926.11967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87415269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.879154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021086
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.2724
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21061
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.861.5970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24921494
X-RAY DIFFRACTIONr_scbond_it2.5143614
X-RAY DIFFRACTIONr_scangle_it3.4294.5536
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 56 -
Rwork0.178 985 -
obs--99.71 %
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)
14.3436-2.07-0.35910.77143.66964.6088-0.00490.20910.2037-0.2629-0.363-0.0273-0.34520.28510.3679-0.0305-0.0853-0.0228-0.0941-0.0001-0.084314.441541.712325.0253
26.32841.18270.01576.40691.32463.8446-0.0375-0.16280.46380.0242-0.22090.5075-0.0817-0.14010.2584-0.0957-0.0370.0281-0.0875-0.045-0.07832.843230.273127.2527
311.2478-5.076-0.90738.69560.30395.7662-0.01720.06470.3363-0.19220.0177-0.0048-0.01730.344-0.0005-0.00870.00550.0273-0.12890.0172-0.1719.912525.67898.696
46.2788-1.0633-1.4033.5559-0.66482.4488-0.1876-0.1895-0.40690.16630.02480.11790.27580.13890.16290.08480.08230.0281-0.16980.0084-0.157819.410112.981119.6081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA145 - 1803 - 38
2X-RAY DIFFRACTION2AA181 - 23539 - 93
3X-RAY DIFFRACTION3BB145 - 1803 - 38
4X-RAY DIFFRACTION4BB181 - 23539 - 93

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