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- PDB-3o6u: Crystal Structure of CPE2226 protein from Clostridium perfringens... -

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Basic information

Entry
Database: PDB / ID: 3o6u
TitleCrystal Structure of CPE2226 protein from Clostridium perfringens. Northeast Structural Genomics Consortium Target CpR195
Componentsuncharacterized protein CPE2226
Keywordsstructural genomics / unknown function / Protein Structure Initiative / NESG / CpR195 / PSI-Biology / Northeast Structural Genomics Consortium / Unknown / Putative FMN-binding protein
Function / homology
Function and homology information


FMN binding / membrane
Similarity search - Function
Major membrane immunogen, tpp15, predicted / Sufe protein. Chain: A - #20 / Sufe protein. Chain: A / FMN-binding / FMN-binding domain / FMN_bind / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FMN-binding domain-containing protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of CPE2226 protein from Clostridium perfringens.
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 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: uncharacterized protein CPE2226
B: uncharacterized protein CPE2226
C: uncharacterized protein CPE2226
D: uncharacterized protein CPE2226
E: uncharacterized protein CPE2226


Theoretical massNumber of molelcules
Total (without water)72,0725
Polymers72,0725
Non-polymers00
Water64936
1
A: uncharacterized protein CPE2226


Theoretical massNumber of molelcules
Total (without water)14,4141
Polymers14,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein CPE2226


Theoretical massNumber of molelcules
Total (without water)14,4141
Polymers14,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: uncharacterized protein CPE2226


Theoretical massNumber of molelcules
Total (without water)14,4141
Polymers14,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: uncharacterized protein CPE2226


Theoretical massNumber of molelcules
Total (without water)14,4141
Polymers14,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: uncharacterized protein CPE2226


Theoretical massNumber of molelcules
Total (without water)14,4141
Polymers14,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.435, 121.643, 95.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsmonomer,15.4 kD,92.7%

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Components

#1: Protein
uncharacterized protein CPE2226


Mass: 14414.472 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CPE2226 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8XI95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 7.5
Details: 3% PEG 3350, 3.46M potassium phosphate, 0.1M HEPES, pH 7.5, Microbatch under Paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 44525 / Num. obs: 44436 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 42.03 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 26.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4471 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→41.675 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.19 / Stereochemistry target values: ML
Details: Molecule E is highly disordered in crystal structure and was built using MR and molecule A as a search model. We speculate this results a higher Rfree factor.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2292 5.17 %RANDOM
Rwork0.204 ---
obs0.208 44368 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.588 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 227.6 Å2 / Biso mean: 55.627 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1--3.905 Å2-0 Å20 Å2
2---8.578 Å20 Å2
3---12.482 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 0 36 4702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094716
X-RAY DIFFRACTIONf_angle_d1.3576320
X-RAY DIFFRACTIONf_chiral_restr0.101706
X-RAY DIFFRACTIONf_plane_restr0.005828
X-RAY DIFFRACTIONf_dihedral_angle_d19.321798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5540.3081530.2482522267597
2.554-2.6140.3061370.24226702807100
2.614-2.6790.3791330.24826282761100
2.679-2.7520.311600.24626312791100
2.752-2.8320.3361300.23126232753100
2.832-2.9240.2641740.22726262800100
2.924-3.0280.3521450.24126342779100
3.028-3.150.3321410.23926482789100
3.15-3.2930.3061500.22626512801100
3.293-3.4660.251490.18926332782100
3.466-3.6840.2531410.17926392780100
3.684-3.9680.2221360.16826702806100
3.968-4.3670.2311360.1626512787100
4.367-4.9970.2081420.14526072749100
4.997-6.2930.2681350.19126622797100
6.293-41.6810.2731300.2042581271197
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)
12.0444-0.42370.55671.8078-0.28170.8165-0.02070.0265-0.0637-0.1455-0.07570.008-0.02240.062200.1465-0.00910.00020.1298-0.01940.060355.536942.573653.7229
22.0045-0.8250.4191.8264-0.25951.03710.10010.1245-0.12350.02160.0920.0690.21380.055500.23190.0375-0.0460.1741-0.00660.156271.060515.978180.4878
31.4413-0.39440.0270.60530.75281.4407-0.08040.0535-0.3358-0.004-0.0697-0.077-0.0521-0.045200.311-0.01180.11760.32760.03880.492779.287121.819350.2232
40.9869-0.64040.49791.5076-1.09261.5412-0.0211-0.0097-0.0131-0.0479-0.01320.11360.1536-0.069800.2230.04110.08110.21660.05810.249773.131857.443429.4121
51.23410.148-0.45221.69240.91541.76440.0109-0.4513-0.2510.29230.0067-0.17480.15580.2239-00.4134-0.0380.02060.65080.01980.4811101.471333.664464.1277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA28 - 149
2X-RAY DIFFRACTION2chain BB28 - 149
3X-RAY DIFFRACTION3chain CC28 - 147
4X-RAY DIFFRACTION4chain DD28 - 148
5X-RAY DIFFRACTION5chain EE28 - 149

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