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- PDB-3kbq: The crystal structure of the protein CinA with unknown function f... -

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Basic information

Entry
Database: PDB / ID: 3kbq
TitleThe crystal structure of the protein CinA with unknown function from Thermoplasma acidophilum
ComponentsProtein Ta0487
Keywordsstructural genomics / unknown function / CinA / Protein Structure Initiative / MCSG / PSI-2 / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Putative competence-damage inducible protein, Archaea / : / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, R. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein CinA with unknown function from Thermoplasma acidophilum
Authors: Zhang, R. / Li, H. / Bearden, J. / Joachimiak, A.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 27, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Protein Ta0487
B: Protein Ta0487
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2013
Polymers37,1052
Non-polymers961
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-26 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.596, 39.718, 55.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThis protein exists as dimer. The deposited MolA/MolB represent the dimer in the asymmetric unit.

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Components

#1: Protein Protein Ta0487


Mass: 18552.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM1728 / Gene: GI:10639657, Ta0487 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HKV6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40% PEG600, 0.1M citrate, pH 5.5, 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: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2→55.99 Å / Num. all: 21287 / Num. obs: 20972 / % possible obs: 98.52 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 23.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.64 / Num. unique all: 1607 / % possible all: 97.64

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→55.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.649 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1128 5.1 %RANDOM
Rwork0.20282 ---
obs0.20479 20972 98.52 %-
all-21287 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→55.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 5 60 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222559
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9923457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40324.73795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71215464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3991514
X-RAY DIFFRACTIONr_chiral_restr0.1190.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211862
X-RAY DIFFRACTIONr_mcbond_it0.9411.51646
X-RAY DIFFRACTIONr_mcangle_it1.72322653
X-RAY DIFFRACTIONr_scbond_it2.9523913
X-RAY DIFFRACTIONr_scangle_it4.7774.5804
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 77 -
Rwork0.224 1492 -
obs-1569 97.64 %
Refinement TLS params.Method: refined / Origin x: 115.197 Å / Origin y: -3.298 Å / Origin z: 44.249 Å
111213212223313233
T0.0829 Å20.0113 Å20.0049 Å2-0.0213 Å2-0.0135 Å2--0.0328 Å2
L1.6167 °2-0.4719 °20.2621 °2-0.702 °2-0.1542 °2--0.9338 °2
S-0.0459 Å °-0.077 Å °-0.0302 Å °-0.0268 Å °0.0599 Å °-0.0312 Å °-0.0231 Å °0.0376 Å °-0.0139 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 166
4X-RAY DIFFRACTION1B-2 - 50
5X-RAY DIFFRACTION1B51 - 100
6X-RAY DIFFRACTION1B101 - 166

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