[English] 日本語
Yorodumi
- PDB-3kh1: Crystal structure of Predicted metal-dependent phosphohydrolase (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kh1
TitleCrystal structure of Predicted metal-dependent phosphohydrolase (ZP_00055740.2) from Magnetospirillum magnetotacticum MS-1 at 1.37 A resolution
ComponentsPredicted metal-dependent phosphohydrolase
KeywordsHYDROLASE / Predicted metal-dependent phosphohydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


5'-deoxynucleotidase activity
Similarity search - Function
HD domain / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Predicted metal-dependent phosphohydrolase
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum MS-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.37 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Predicted metal-dependent phosphohydrolase (ZP_00055740.2) from Magnetospirillum magnetotacticum MS-1 at 1.37 A resolution ;
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 25, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Polymer sequence / Refinement description / Source and taxonomy
Category: entity_poly / entity_src_gen ...entity_poly / entity_src_gen / pdbx_database_related / pdbx_distant_solvent_atoms / pdbx_struct_assembly_auth_evidence / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_poly.pdbx_target_identifier / _entity_src_gen.pdbx_beg_seq_num ..._entity_poly.pdbx_target_identifier / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_related.db_id / _software.classification / _software.name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code
Revision 2.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Predicted metal-dependent phosphohydrolase
B: Predicted metal-dependent phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7835
Polymers45,4902
Non-polymers2933
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-42 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.852, 83.906, 71.278
Angle α, β, γ (deg.)90.00, 116.89, 90.00
Int Tables number5
Space group name H-MC121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

-
Components

#1: Protein Predicted metal-dependent phosphohydrolase


Mass: 22745.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum MS-1 (bacteria)
Gene: ZP_00055740.2 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: D1MPT5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE FROM GENBANK WITH ACCESSION CODE ZP_00055740.2 AND FROM THE UNIPROT ARCHIVE (UNIPARC) WITH ACCESSION CODE UPI00003847C7.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.24 %
Description: THE STATISTICS REPORTED IN REMARK 200 WERE COMPUTED WITH XSCALE WITH FRIEDEL PAIRS KEPT SEPARATE.
Crystal growTemperature: 277 K / pH: 7.67
Details: 20.0000% polyethylene glycol 3000, 0.2500M calcium acetate, 0.1M TRIS pH 7.67, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.978985
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2009 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978985 Å / Relative weight: 1
ReflectionResolution: 1.37→41.959 Å / Num. obs: 85080 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.68 Å2
Reflection shellResolution: 1.37→1.42 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.2 / % possible all: 97.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.37→41.96 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.667 / SU ML: 0.03 / ESU R: 0.051 / ESU R Free: 0.049
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ACETATE (ACT), CALCIUM (CA), AND A PEG-200 FRAGMENT (PG4) FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflection
Rfree0.164 4252 5 %
Rwork0.132 --
obs0.133 85080 99.5 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å2-0.18 Å2
2--1.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.37→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 12 515 3690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223254
X-RAY DIFFRACTIONr_bond_other_d0.0010.022258
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.964442
X-RAY DIFFRACTIONr_angle_other_deg0.90535462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5215432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66522.378164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02915557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9761542
X-RAY DIFFRACTIONr_chiral_restr0.0740.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02720
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.52002
X-RAY DIFFRACTIONr_mcbond_other0.2341.5798
X-RAY DIFFRACTIONr_mcangle_it1.23623215
X-RAY DIFFRACTIONr_scbond_it2.11431252
X-RAY DIFFRACTIONr_scangle_it3.1554.51202
X-RAY DIFFRACTIONr_rigid_bond_restr0.73635511
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.41 Å
RfactorNum. reflection% reflection
Rfree0.216 302 -
Rwork0.191 5811 -
obs--97.78 %
Refinement TLS params.

T13: 0.0047 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.628-0.39410.23320.5144-0.0850.8463-0.0059-0.1181-0.18810.04350.02880.07550.0506-0.1016-0.02290.0477-0.00740.01750.01320.04120.604944.696119.0795
21.352-0.17680.36020.6661-0.02891.02610.01030.16060.0742-0.0347-0.0308-0.1112-0.04710.25540.02050.0453-0.01290.06850.01330.043419.805851.688711.3976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 90
2X-RAY DIFFRACTION1A94 - 199
3X-RAY DIFFRACTION2B6 - 88
4X-RAY DIFFRACTION2B94 - 199

+
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