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- PDB-2hx0: Three-dimensional structure of the hypothetical protein from Salm... -

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Basic information

Entry
Database: PDB / ID: 2hx0
TitleThree-dimensional structure of the hypothetical protein from Salmonella cholerae-suis (aka Salmonella enterica) at the resolution 1.55 A. Northeast Structural Genomics target ScR59.
ComponentsPutative DNA-binding protein
KeywordsDNA BINDING PROTEIN / NESG / PSI-2 / ScR59 / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
PPC 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; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative DNA-binding protein
Similarity search - Component
Biological speciesSalmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, J. / Shastry, R. / Conover, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Shastry, R. / Conover, 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: Three-dimensional structure of the hypothetical protein from Salmonella cholerae-suis (aka Salmonella enterica) at the resolution 1.55 A. Northeast Structural Genomics target ScR59.
Authors: Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Shastry, R. / Conover, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G. / Tong, L. / Hunt, J.F. / ...Authors: Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Shastry, R. / Conover, 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)
History
DepositionAug 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999AUTHORS STATE THAT THERE IS MOST LIKELY A POLYMORPHISM OR AN ERROR IN THE ORIGINAL GENOME SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9712
Polymers16,9461
Non-polymers241
Water2,144119
1
A: Putative DNA-binding protein
hetero molecules

A: Putative DNA-binding protein
hetero molecules

A: Putative DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9126
Polymers50,8393
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7720 Å2
ΔGint-83 kcal/mol
Surface area15150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.759, 78.759, 45.926
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

Detailstrimer, formed by operation symmetry/translation: 2 0 -1 0 3 1 0 0

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Components

#1: Protein Putative DNA-binding protein


Mass: 16946.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q57K43
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM Magnesium formate, 18% PEG3350, 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: Jul 23, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 46161 / Num. obs: 46085 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 40.5
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→19.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 381920.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2109 4.9 %RANDOM
Rwork0.197 ---
obs0.197 42649 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.5354 Å2 / ksol: 0.341776 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.98 Å20 Å2
2--1.27 Å20 Å2
3----2.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 1 119 1168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 288 4.9 %
Rwork0.223 5639 -
obs--77.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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