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- PDB-4hbz: The Structure of Putative Phosphohistidine Phosphatase SixA from ... -

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Basic information

Entry
Database: PDB / ID: 4hbz
TitleThe Structure of Putative Phosphohistidine Phosphatase SixA from Nakamurella multipartitia.
ComponentsPutative phosphohistidine phosphatase, SixA
KeywordsHYDROLASE / ISOMERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / HP_PGM_like / PFAM / Phosphoglycerate mutase
Function / homology
Function and homology information


Phosphoglycerate mutase-like / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / TRIETHYLENE GLYCOL / Putative phosphohistidine phosphatase, SixA
Similarity search - Component
Biological speciesNakamurella multipartita (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsCuff, M.E. / Holowicki, J. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The Structure of Putative Phosphohistidine Phosphatase SixA from Nakamurella multipartitia.
Authors: Cuff, M.E. / Holowicki, J. / Endres, M. / Joachimiak, A.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Oct 9, 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 / struct_site
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 / _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: Putative phosphohistidine phosphatase, SixA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6986
Polymers19,2431
Non-polymers4545
Water3,729207
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.257, 76.257, 50.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

21A-356-

HOH

31A-405-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Putative phosphohistidine phosphatase, SixA


Mass: 19243.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nakamurella multipartita (bacteria) / Strain: DSM 44233 / Gene: Namu_4970 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C8XA43
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris:HCl pH 8.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 19, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionRedundancy: 12.5 % / Av σ(I) over netI: 47.19 / Number: 280670 / Rmerge(I) obs: 0.07 / Χ2: 1.43 / D res high: 1.55 Å / D res low: 50 Å / Num. obs: 22385 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.215099.210.0482.63912.5
3.344.2110010.0411.87313.9
2.923.3410010.051.81814.2
2.652.9210010.0571.69614.3
2.462.6510010.0681.62514.3
2.322.4610010.0781.52814.4
2.22.3210010.0811.46414.4
2.12.210010.0951.3914.4
2.022.110010.1111.34614.5
1.952.0210010.1311.29714.4
1.891.9510010.1671.25414.4
1.841.8910010.1931.23614.4
1.791.8410010.2481.19913.8
1.751.7910010.2811.10812.5
1.711.7510010.3471.05111.7
1.671.7110010.4041.09511
1.641.6710010.4171.03210.2
1.611.6410010.4830.9628.3
1.581.6110010.5150.9827
1.551.5810010.5830.9875.9
ReflectionResolution: 1.55→50 Å / Num. all: 22385 / Num. obs: 22385 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.434 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.585.90.58310920.9871100
1.58-1.6170.51510900.9821100
1.61-1.648.30.48311050.9621100
1.64-1.6710.20.41710831.0321100
1.67-1.71110.40411011.0951100
1.71-1.7511.70.34711041.0511100
1.75-1.7912.50.28110921.1081100
1.79-1.8413.80.24811031.1991100
1.84-1.8914.40.19311201.2361100
1.89-1.9514.40.16711111.2541100
1.95-2.0214.40.13110891.2971100
2.02-2.114.50.11111031.3461100
2.1-2.214.40.09511221.391100
2.2-2.3214.40.08111241.4641100
2.32-2.4614.40.07811181.5281100
2.46-2.6514.30.06811321.6251100
2.65-2.9214.30.05711301.6961100
2.92-3.3414.20.0511421.8181100
3.34-4.2113.90.04111681.8731100
4.21-5012.50.04812562.639199.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.404 / FOM acentric: 0.488 / FOM centric: 0 / Reflection: 10600 / Reflection acentric: 8776 / Reflection centric: 1824
Phasing MAD setR cullis acentric: 1.97 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 8776 / Reflection centric: 1824
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.5-507.950.40.11938
7.14-12.52.150.20.112390
5-7.142.180.10.1336148
3.85-51.30.10.1638198
3.13-3.851.440.10.11059263
2.63-3.132.030.101551303
2.27-2.632.40.102176369
2-2.272.290.102874415
Phasing MAD set siteAtom type symbol: Se / B iso: 23.1311 / Fract x: -0.976 / Fract y: -0.271 / Fract z: -0.116 / Occupancy: 4.335 / Occupancy iso: 0
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.1380.4130571938
7.14-12.50.2540.439021312390
5-7.140.3860.5560484336148
3.85-50.4290.5620836638198
3.13-3.850.4410.55013221059263
2.63-3.130.4420.529018541551303
2.27-2.630.4120.482025452176369
2-2.270.3730.427032892874415
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 22293
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.73-10066.70.555504
4.51-5.7364.40.905509
3.92-4.51600.908501
3.54-3.9262.30.893506
3.27-3.5461.50.906539
3.04-3.2758.40.889571
2.86-3.04630.887615
2.71-2.8664.10.888633
2.58-2.7161.70.89691
2.46-2.5864.30.894698
2.37-2.4660.30.883735
2.28-2.37650.891763
2.2-2.2860.30.907784
2.13-2.262.40.889811
2.06-2.1364.70.888844
2-2.0665.40.879868
1.95-285.90.863888
1.9-1.9594.50.851894
1.85-1.9890.854944
1.81-1.8589.70.84948
1.77-1.8190.20.837968
1.73-1.7789.60.825991
1.69-1.7389.60.831013
1.66-1.6991.20.7561035
1.63-1.6689.60.8041048
1.6-1.6389.60.7081084
1.55-1.688.10.541908

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.55→38.16 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1492 / WRfactor Rwork: 0.1311 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.923 / SU B: 2.284 / SU ML: 0.041 / SU R Cruickshank DPI: 0.072 / SU Rfree: 0.0692 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.069
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1614 1142 5.1 %RANDOM
Rwork0.1411 ---
all0.1421 22327 --
obs0.1421 22327 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.12 Å2 / Biso mean: 20.5455 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.55→38.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 30 207 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191385
X-RAY DIFFRACTIONr_bond_other_d0.0030.021320
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9531900
X-RAY DIFFRACTIONr_angle_other_deg0.8963.0033013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.44122.14356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74715185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8591515
X-RAY DIFFRACTIONr_chiral_restr0.1020.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 87 -
Rwork0.214 1533 -
all-1620 -
obs--99.33 %
Refinement TLS params.Method: refined / Origin x: 18.0306 Å / Origin y: 36.2715 Å / Origin z: 13.7516 Å
111213212223313233
T0.0178 Å20.0029 Å2-0.001 Å2-0.0144 Å20.0081 Å2--0.015 Å2
L0.8012 °20.3162 °2-0.0233 °2-0.4807 °2-0.1542 °2--0.7991 °2
S-0.0355 Å °-0.0281 Å °-0.0252 Å °-0.0126 Å °-0.0099 Å °-0.0628 Å °-0.0279 Å °-0.0279 Å °0.0454 Å °

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