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- PDB-2nmu: Crystal structure of the hypothetical protein from Salmonella typ... -

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Basic information

Entry
Database: PDB / ID: 2nmu
TitleCrystal structure of the hypothetical protein from Salmonella typhimurium LT2. Northeast Structural Genomics Consortium target StR127.
ComponentsPutative DNA-binding protein
KeywordsDNA BINDING PROTEIN / NESG X-Ray Q8ZM67 StR127 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyPPC domain / Plants and Prokaryotes Conserved (PCC) domain / PPC domain profile profile. / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / DNA binding / 2-Layer Sandwich / Alpha Beta / Putative DNA-binding protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the hypothetical protein from Salmonella typhimurium LT2. Northeast Structural Genomics Consortium target StR127.
Authors: Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G. / Tong, L. / Hunt, J.F.
History
DepositionOct 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)17,2231
Polymers17,2231
Non-polymers00
Water1,36976
1
A: Putative DNA-binding protein

A: Putative DNA-binding protein

A: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)51,6683
Polymers51,6683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7570 Å2
ΔGint-52 kcal/mol
Surface area14900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.871, 78.871, 44.256
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Putative DNA-binding protein


Mass: 17222.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: STM3071 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZM67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8M K,Na-Tartrate, 0.1M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2006 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28283 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 16.6 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.3
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.6 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HX0

2hx0


Resolution: 1.8→37.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 110515.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1338 4.9 %RANDOM
Rwork0.185 ---
all0.185 27394 --
obs0.185 27394 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.9128 Å2 / ksol: 0.407711 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.67 Å20 Å2
2---0.16 Å20 Å2
3---0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 0 76 1114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 214 5.1 %
Rwork0.227 4015 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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