[English] 日本語
Yorodumi
- PDB-2rd9: Crystal structure of a putative yfit-like metal-dependent hydrola... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rd9
TitleCrystal structure of a putative yfit-like metal-dependent hydrolase (bh0186) from bacillus halodurans c-125 at 2.30 A resolution
ComponentsBH0186 protein
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


DinB-like domain / DinB superfamily / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / NICKEL (II) ION / BH0186 protein
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of YfiT-like putative metal-dependent hydrolase (NP_241052.1) from Bacillus halodurans at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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 300 BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BH0186 protein
B: BH0186 protein
C: BH0186 protein
D: BH0186 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,78620
Polymers91,5614
Non-polymers1,22516
Water9,998555
1
A: BH0186 protein
B: BH0186 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,47311
Polymers45,7802
Non-polymers6939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
MethodPISA
2
C: BH0186 protein
D: BH0186 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3129
Polymers45,7802
Non-polymers5327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.330, 147.330, 147.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISALAAA-11 - 758 - 94
21HISALABB-11 - 758 - 94
31HISALACC-11 - 758 - 94
41HISALADD-11 - 758 - 94
12ALAASPAA87 - 174106 - 193
22ALAASPBB87 - 174106 - 193
32ALAASPCC87 - 174106 - 193
42ALAASPDD87 - 174106 - 193

NCS ensembles :
ID
1
2
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein
BH0186 protein


Mass: 22890.209 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: NP_241052.1, BH0186 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9KGB8
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NANODROP, 10.0% PEG 6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97941
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
ReflectionResolution: 2.3→29.463 Å / Num. obs: 47316 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.076 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.51
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.380.3363.1246148684197.3
2.38-2.480.2883.7278059656199.9
2.48-2.590.2314.62561188851100
2.59-2.730.1925.62713094051100
2.73-2.90.1427.4262709091199.9
2.9-3.120.09910.6259438963199.9
3.12-3.430.06415.8265029150199.9
3.43-3.930.0521.4262929243199.8
3.93-4.930.02734262819087199.9
4.93-29.4630.02238.6263349196198.5

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.463 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.357 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.185
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 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. RESIDUES 77-84 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. A NICKEL ION IS COORDINATED IN AN OCTAHEDRAL COMPLEX TO THE SIDECHAINS OF HIS48, HIS142 AND HIS146 ON THE SAME CHAIN, HIS-9 ON THE NEIGHBORING CHAIN, AND ONE IMIDAZOLE AND ONE WATER MOLECULES. X-RAY FLUORESCENCE SUPPORTS THE ASSIGNMENT OF THE NICKEL ION. 5. IMIDAZOLE MOLECULES FROM THE PURIFICATION SOLUTION ARE MODELED. 6. GLYCEROL MOLECULES FROM THE CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2393 5.1 %RANDOM
Rwork0.152 ---
obs0.155 47291 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 71 555 6846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216549
X-RAY DIFFRACTIONr_bond_other_d0.0020.024456
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9278874
X-RAY DIFFRACTIONr_angle_other_deg0.944310782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8823.814354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.271151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6931545
X-RAY DIFFRACTIONr_chiral_restr0.0790.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021416
X-RAY DIFFRACTIONr_nbd_refined0.210.21442
X-RAY DIFFRACTIONr_nbd_other0.1970.24799
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23157
X-RAY DIFFRACTIONr_nbtor_other0.090.23183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2476
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.29
X-RAY DIFFRACTIONr_mcbond_it1.81934163
X-RAY DIFFRACTIONr_mcbond_other0.54631517
X-RAY DIFFRACTIONr_mcangle_it2.49956167
X-RAY DIFFRACTIONr_scbond_it4.72583035
X-RAY DIFFRACTIONr_scangle_it6.074112707
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1182MEDIUM POSITIONAL0.350.5
12B1182MEDIUM POSITIONAL0.330.5
13C1182MEDIUM POSITIONAL0.40.5
14D1182MEDIUM POSITIONAL0.380.5
11A1182MEDIUM THERMAL0.972
12B1182MEDIUM THERMAL0.942
13C1182MEDIUM THERMAL1.072
14D1182MEDIUM THERMAL0.922
21A1154MEDIUM POSITIONAL0.240.5
22B1154MEDIUM POSITIONAL0.20.5
23C1154MEDIUM POSITIONAL0.240.5
24D1154MEDIUM POSITIONAL0.240.5
21A1154MEDIUM THERMAL0.932
22B1154MEDIUM THERMAL0.862
23C1154MEDIUM THERMAL0.972
24D1154MEDIUM THERMAL0.952
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 196 -
Rwork0.172 3188 -
all-3384 -
obs--97.27 %
Refinement TLS params.

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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82550.22750.24340.55510.0960.9864-0.0052-0.10220.12270.12270.02250.0658-0.0361-0.0093-0.0174-0.07670.0070.0169-0.0322-0.0016-0.061199.27446.7467125.118
20.85950.3564-0.32520.921-0.30770.8517-0.0149-0.0730.0630.13640.03830.23960.0559-0.0987-0.0234-0.0322-0.0005-0.003-0.01830.0292-0.063686.8129-10.533123.7013
30.5904-0.1516-0.05490.86830.10411.09040.00490.0318-0.0157-0.08190.034-0.00990.14590.0134-0.0389-0.07290.0199-0.0298-0.05050.0104-0.099699.3942-8.21393.1643
40.4976-0.36670.18290.9681-0.25090.74840.06350.04390.0119-0.1185-0.03190.210.0685-0.0778-0.0316-0.09440.004-0.0109-0.04460.0175-0.045886.52719.793794.7833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-14 - 1745 - 193
2X-RAY DIFFRACTION2BB-15 - 1744 - 193
3X-RAY DIFFRACTION3CC-11 - 1748 - 193
4X-RAY DIFFRACTION4DD-14 - 1745 - 193

+
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