[English] 日本語
Yorodumi
- PDB-4hbz: The Structure of Putative Phosphohistidine Phosphatase SixA from ... -

+
Open data


ID or keywords:

Loading...

-
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 family / Phosphoglycerate mutase-like / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

-
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 °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more