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- PDB-3me8: Crystal structure of putative electron transfer protein aq_2194 f... -

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Basic information

Entry
Database: PDB / ID: 3me8
TitleCrystal structure of putative electron transfer protein aq_2194 from Aquifex aeolicus VF5
ComponentsPutative uncharacterized protein
KeywordsELECTRON TRANSPORT / electron transfer protein / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
Copper chaperone SCO1/SenC / SCO1/SenC / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative electron transfer protein aq_2194 from Aquifex aeolicus VF5
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 21, 2018Group: Data collection / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,8132
Polymers38,8132
Non-polymers00
Water5,495305
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,4061
Polymers19,4061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,4061
Polymers19,4061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.574, 134.767, 37.333
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-107-

PHE

Detailsauthors state that this is an uncharacterized protein. It might form a dimer by applying -x,-y,z symmetry operation on chain A.

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Components

#1: Protein Putative uncharacterized protein


Mass: 19406.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_2194, NP_214507.1 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: O67938
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 100mM CHES, 1M Sodium Citrate dihydrate, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2010
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 53622 / % possible obs: 94.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Χ2: 1.094 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.5330.5734790.772165.4
1.53-1.553.20.49638350.762171.4
1.55-1.583.20.48840560.792176.9
1.58-1.623.40.4644980.789183.7
1.62-1.653.50.45847920.822190.3
1.65-1.693.60.41151810.826195.6
1.69-1.733.60.37252850.815199.1
1.73-1.783.80.31754070.8481100
1.78-1.833.80.25552710.8571100
1.83-1.893.80.20253580.8761100
1.89-1.963.80.15754110.9321100
1.96-2.043.80.12652601.0071100
2.04-2.133.80.09953791.0661100
2.13-2.243.80.07853471.1181100
2.24-2.383.80.06953421.1751100
2.38-2.563.80.06953511.4781100
2.56-2.823.80.06753851.8491100
2.82-3.233.80.05253351.8861100
3.23-4.073.70.03153741.3261100
4.07-503.90.02853561.236199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.855 / SU B: 3.477 / SU ML: 0.057 / SU R Cruickshank DPI: 0.08 / SU Rfree: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2718 5.1 %RANDOM
Rwork0.188 ---
obs0.19 53622 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.04 Å2 / Biso mean: 18.993 Å2 / Biso min: 8.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å20 Å2
2---1.07 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 0 305 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222743
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9713728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46324.083120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90615485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7191510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212053
X-RAY DIFFRACTIONr_mcbond_it1.0033.51638
X-RAY DIFFRACTIONr_mcangle_it2.803502673
X-RAY DIFFRACTIONr_scbond_it5.123501105
X-RAY DIFFRACTIONr_scangle_it1.3234.51048
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 162 -
Rwork0.294 2762 -
all-2924 -
obs--72.13 %
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)
10.6903-0.1210.03471.0807-0.01210.7142-0.0057-0.0366-0.0528-0.0117-0.00920.0592-0.0214-0.06170.0150.00580.011-0.00240.02280.00050.0289-10.254513.261111.6443
20.77080.14720.03430.88150.0981.70310.00020.0196-0.0049-0.06980.0127-0.0560.0780.1564-0.01290.0384-0.01210.00940.0287-0.00110.018517.757823.197812.1259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 170
2X-RAY DIFFRACTION2B2 - 163

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