[English] 日本語
Yorodumi
- PDB-1vrb: Crystal structure of Putative asparaginyl hydroxylase (2636534) f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vrb
TitleCrystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution
ComponentsPutative asparaginyl hydroxylase
KeywordsOXIDOREDUCTASE / 2636534 / putative asparaginyl hydroxylase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #40 / JmjC domain-containing / JmjC domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Helix non-globular / Special ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #40 / JmjC domain-containing / JmjC domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Helix non-globular / Special / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Uncharacterized protein YxbC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: 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_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative asparaginyl hydroxylase
B: Putative asparaginyl hydroxylase
C: Putative asparaginyl hydroxylase
D: Putative asparaginyl hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,3568
Polymers157,1324
Non-polymers2234
Water39622
1
A: Putative asparaginyl hydroxylase
B: Putative asparaginyl hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6784
Polymers78,5662
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-83 kcal/mol
Surface area24160 Å2
MethodPISA
2
C: Putative asparaginyl hydroxylase
D: Putative asparaginyl hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6784
Polymers78,5662
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-78 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.300, 104.660, 286.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVALAA8 - 6620 - 78
21VALVALVALVALBB8 - 6620 - 78
31VALVALVALVALCC8 - 6620 - 78
41SERSERVALVALDD7 - 6619 - 78
52ALAALATHRTHRAA96 - 326108 - 338
62ALAALATHRTHRBB96 - 326108 - 338
72ALAALATHRTHRCC97 - 326109 - 338
82ALAALATHRTHRDD96 - 326108 - 338

-
Components

#1: Protein
Putative asparaginyl hydroxylase


Mass: 39283.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yxbC / Production host: Escherichia coli (E. coli) / References: UniProt: P46327
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2645.49
22.855.79
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting drop, nanodrop24% NP_PEG 4000, 0.065M Tris_base, 0.16M Mg Cl, 0.035M Tris Cl, 20% Glycerol, CuCl2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
2932vapor diffusion, sitting drop, nanodrop24% NP_PEG 4000, 0.065M Tris_base, 0.16M Mg Cl, 0.035M Tris Cl, 20% Glycerol, CuCl2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.111.0332
SYNCHROTRONALS 8.3.120.979686, 0.979835, 1.020026
Detector
TypeIDDetectorDate
ADSC1CCDSep 22, 2003
ADSC2CCDSep 11, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.9796861
30.9798351
41.0200261
ReflectionResolution: 2.5→28.66 Å / Num. obs: 49807 / % possible obs: 98.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 82.46 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6756 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
XDSdata scaling
SCALAdata scaling
SHELXD+ AutoSHARPphasing
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→28.66 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 29.814 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.701 / ESU R Free: 0.333
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.THE DENSITIES FOR THE FOLLOWING REGIONS, 66-96, 178-185, 268-275, 138-142, ARE VERY POOR. ALTHOUGH MODEL WAS BUILT FOR SOME OF THESE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.THE DENSITIES FOR THE FOLLOWING REGIONS, 66-96, 178-185, 268-275, 138-142, ARE VERY POOR. ALTHOUGH MODEL WAS BUILT FOR SOME OF THESE REGIONS, THEY MAY CONTAIN ERRORS. 3.A FERRIC IRON IS MODELLED FOR EACH CHAIN. THIS ASSIGNMENT WAS BASED ON HOMOLOGS (1IZ3 AND 1MZE). HOWEVER, THIS CRYSTAL WAS OBTAINED IN BUFFER CONTAINING COPPER. THERE IS NO EVIDENCE TO EXCLUED THE POSSIBILITY THE ION BEING OTHER METALS SUCH AS COPPER. 4.D278-D285 IS A PART OF HELIX, THE REFINEMENT OF THIS REGION IS NOT STABLE DUE TO THE POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27227 2243 5 %RANDOM
Rwork0.22144 ---
obs0.22399 42483 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.826 Å2
Baniso -1Baniso -2Baniso -3
1-6 Å20 Å20 Å2
2---1.49 Å20 Å2
3----4.51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9010 0 4 22 9036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229238
X-RAY DIFFRACTIONr_bond_other_d0.0030.028381
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.95512683
X-RAY DIFFRACTIONr_angle_other_deg0.873319097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58251210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59423.814333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.325151229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5231532
X-RAY DIFFRACTIONr_chiral_restr0.0850.21503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021893
X-RAY DIFFRACTIONr_nbd_refined0.2480.22192
X-RAY DIFFRACTIONr_nbd_other0.1840.28428
X-RAY DIFFRACTIONr_nbtor_other0.0920.25795
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.218
X-RAY DIFFRACTIONr_mcbond_it1.53536211
X-RAY DIFFRACTIONr_mcbond_other0.49232436
X-RAY DIFFRACTIONr_mcangle_it2.34159680
X-RAY DIFFRACTIONr_scbond_it4.20683506
X-RAY DIFFRACTIONr_scangle_it5.77113003
X-RAY DIFFRACTIONr_nbtor_refined0.1990.24606
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0190.21
Refine LS restraints NCS

Ens-ID: 1 / Number: 3934 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.570.5
2Bmedium positional0.690.5
3Cmedium positional0.510.5
4Dmedium positional0.570.5
1Amedium thermal0.852
2Bmedium thermal0.812
3Cmedium thermal0.732
4Dmedium thermal0.782
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 164 5.29 %
Rwork0.37 2935 -
obs--94.57 %
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)
10.96580.8532.15211.24451.43355.7188-0.1093-0.0946-0.15210.24320.0065-0.0583-0.28480.42120.1029-0.33460.0411-0.0333-0.01190.0477-0.00762.988449.2048137.6508
27.76162.33743.731529.5456-2.99388.48040.16530.18990.8711-0.6785-0.54860.1261-1.980.53360.3833-0.0152-0.0822-0.1021-0.011-0.01930.005761.250172.6009140.3909
30.96840.3290.10412.7242-1.58483.5815-0.05690.1550.0012-0.0736-0.1613-0.0762-0.24530.13590.2183-0.32090.0422-0.0711-0.20230.0313-0.106852.798755.6551112.2554
46.06992.14942.58344.81352.533610.6777-0.57980.05861.0683-0.1683-0.01-0.8815-0.12321.09220.58990.0038-0.0082-0.0898-0.08190.17990.19867.949275.8987116.1472
50.60680.256-0.41341.5974-0.65543.9768-0.0936-0.2231-0.07110.3258-0.0590.06330.1365-0.36090.1526-0.0576-0.0047-0.0561-0.06060.0531-0.083841.735162.46666.9471
645.149510.2192-3.728731.3911-13.490835.91450.04820.2194-1.4244-1.16691.13170.78863.55221.9192-1.17990.01840.08910.05680.01430.1036-0.04952.330440.246568.8953
71.209-0.5291-0.77562.44891.7654.7634-0.17070.2393-0.12670.1608-0.0249-0.20570.2762-0.03890.1956-0.2954-0.0688-0.0455-0.18910.0455-0.063752.565559.335141.2205
84.38828.7267-3.121222.6560.09199.70420.45970.1964-0.55250.7512-0.31310.37582.2495-1.3372-0.14650.0733-0.12120.08510.0604-0.01730.290146.554337.046344.6474
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA8 - 6620 - 78
21AA95 - 326107 - 338
32AA80 - 9492 - 106
43BB8 - 6620 - 78
53BB95 - 326107 - 338
64BB67 - 9479 - 106
75CC8 - 6620 - 78
85CC97 - 326109 - 338
106CC80 - 9392 - 105
117DD8 - 6620 - 78
127DD95 - 326107 - 338
138DD67 - 9479 - 106

+
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