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- PDB-3p51: Three-dimensional structure of protein Q2Y8N9_NITMU from nitrosos... -

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Basic information

Entry
Database: PDB / ID: 3p51
TitleThree-dimensional structure of protein Q2Y8N9_NITMU from nitrosospira multiformis, Northeast structural genomics consortium target NMR118
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 / Polyketide cyclase / dehydrase and lipid transport
Function and homology information
Biological speciesNitrosospira multiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.056 Å
AuthorsKuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / 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 NmR118
Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 7, 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / 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 / _entity_src_gen.pdbx_host_org_scientific_name / _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


Theoretical massNumber of molelcules
Total (without water)18,4181
Polymers18,4181
Non-polymers00
Water2,558142
1
A: Uncharacterized protein

A: Uncharacterized protein

A: Uncharacterized protein

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)73,6724
Polymers73,6724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area4550 Å2
ΔGint-32 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.409, 80.409, 108.256
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

21A-298-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 18417.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosospira multiformis (bacteria) / Strain: ATCC 25196 / NCIMB 11849 / Gene: Nmul_A1581 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q2Y8N9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: macrobatch under oil / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: LiCl 4.42M, Bis-Tris Propane 0.1M, macrobatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 23884 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 39.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 / % possible all: 83.3

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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: 2.056→40.204 Å / FOM work R set: 0.84 / Cross valid method: THROUGHOUT / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1229 10.01 %5%
Rwork0.191 ---
obs0.194 13511 91.3 %-
Solvent computationShrinkage radii: 0.95 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.833 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 128.04 Å2 / Biso mean: 45.23 Å2 / Biso min: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1-5.295 Å20 Å2-0 Å2
2--5.295 Å20 Å2
3----10.589 Å2
Refinement stepCycle: LAST / Resolution: 2.056→40.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 0 142 1288
Refinement TLS params.Method: refined / Origin x: 24.9863 Å / Origin y: 18.729 Å / Origin z: 63.3293 Å
111213212223313233
T0.3621 Å2-0.0536 Å20.0444 Å2-0.2632 Å2-0.0089 Å2--0.2332 Å2
L1.3958 °2-0.4318 °2-0.3832 °2-0.5803 °20.6197 °2--0.6956 °2
S-0.1437 Å °0.1651 Å °-0.0943 Å °-0.0179 Å °-0.0021 Å °0.0505 Å °0.2048 Å °0.0199 Å °0.134 Å °
Refinement TLS groupSelection details: all

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