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- PDB-3p9v: High Resolution Crystal Structure of protein Maqu_3174 from Marin... -

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Basic information

Entry
Database: PDB / ID: 3p9v
TitleHigh Resolution Crystal Structure of protein Maqu_3174 from Marinobacter aquaeolei, Northeast Structural Genomics Consortium Target MqR197
ComponentsUncharacterized protein
KeywordsStructural genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / SRPBCC family protein
Function and homology information
Biological speciesMarinobacter aquaeolei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsKuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / 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: Northeast Structural Genomics Consortium Target MqR197
Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / 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
DepositionOct 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)35,9442
Polymers35,9442
Non-polymers00
Water6,648369
1
A: Uncharacterized protein

B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)35,9442
Polymers35,9442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area1460 Å2
ΔGint-16 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.260, 55.600, 102.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 17971.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter aquaeolei (bacteria) / Strain: ATCC 700491 / DSM 11845 / VT8 / Gene: Maqu_3174 / Production host: Escherichia coli (E. coli) / References: UniProt: A1U5H9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 293 K / Method: macrobatch under oil / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution:ammonium thiocyanate 0.1M, MES 0.1M, PEG 4000 20% (W/V), macrobatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 55882 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.6
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4440 / % possible all: 75.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→26.828 Å / FOM work R set: 0.853 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1999 7.28 %5.0%
Rwork0.197 ---
obs0.2 29458 88.8 %-
Solvent computationShrinkage radii: 0.83 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.605 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 124.87 Å2 / Biso mean: 30.37 Å2 / Biso min: 10.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å2-0 Å2
2--0.664 Å20 Å2
3----1.924 Å2
Refinement stepCycle: LAST / Resolution: 1.78→26.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 0 369 2776
Refinement TLS params.Method: refined / Origin x: 42.0796 Å / Origin y: 38.7237 Å / Origin z: 74.5092 Å
111213212223313233
T0.126 Å2-0.0134 Å20.0092 Å2-0.1195 Å20.0052 Å2--0.1445 Å2
L0.2794 °2-0.1299 °20.2786 °2-0.2457 °2-0.1665 °2--0.7257 °2
S0.0385 Å °-0.0434 Å °0.0578 Å °-0.0072 Å °0.045 Å °0.0316 Å °0.0745 Å °-0.0692 Å °-0.0744 Å °
Refinement TLS groupSelection details: all

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