[English] 日本語
Yorodumi
- PDB-1w9a: Crystal structure of Rv1155 from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w9a
TitleCrystal structure of Rv1155 from Mycobacterium tuberculosis
ComponentsPUTATIVE PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / RELATED TO FMN-BINDING PROTEINS
Function / homology
Function and homology information


vitamin B6 metabolic process / coenzyme F420 binding / oxidoreductase activity, acting on the CH-CH group of donors / Oxidoreductases / pyridoxal phosphate binding / FMN binding / protein homodimerization activity
Similarity search - Function
F420-binding domain, putative / : / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
F420H(2)-dependent reductase Rv1155
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsCannan, S. / Sulzenbacher, G. / Roig-Zamboni, V. / Scappuccini, L. / Frassinetti, F. / Maurien, D. / Cambillau, C. / Bourne, Y.
CitationJournal: FEBS Lett. / Year: 2005
Title: Crystal Structure of the Conserved Hypothetical Protein Rv1155 from Mycobacterium Tuberculosis
Authors: Canaan, S. / Sulzenbacher, G. / Roig-Zamboni, V. / Scappuccini-Calvo, L. / Frassinetti, F. / Maurin, D. / Cambillau, C. / Bourne, Y.
History
DepositionOct 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 6, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2013Group: Data collection / Other ...Data collection / Other / Source and taxonomy / Structure summary
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE
B: PUTATIVE PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE


Theoretical massNumber of molelcules
Total (without water)32,9242
Polymers32,9242
Non-polymers00
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.953, 55.122, 55.231
Angle α, β, γ (deg.)90.00, 108.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.61749, -0.74038, -0.2656), (-0.70492, 0.37106, 0.60449), (-0.349, 0.56049, -0.75103)
Vector: 3.7761, 2.11774, 35.50867)

-
Components

#1: Protein PUTATIVE PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE / PNP/PMP OXIDASE / PNPOX / RV1155 / PYRIDOXAL 5'-PHOSPHATE SYNTHASE


Mass: 16462.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: HISPKM596 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: O06553, pyridoxal 5'-phosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.1 Å3/Da / Density % sol: 40.7 %
Crystal growpH: 7.5 / Details: 15 % (W/V) PEG 6000 0.1 M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95373
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 12, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.8→38 Å / Num. obs: 24197 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.48 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.7 / % possible all: 95

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.372 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE TOTAL B VALUES, SUM OF TLS COMPONENT AND RESIDUAL, ARE GIVEN FOR EACH ATOM
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1429 5.9 %RANDOM
Rwork0.141 ---
obs0.143 22732 97.1 %-
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: 18.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20.1 Å2
2---0.52 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 0 371 2596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222350
X-RAY DIFFRACTIONr_bond_other_d0.0040.022227
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9743215
X-RAY DIFFRACTIONr_angle_other_deg0.80435162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.01822.936109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82715398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.931525
X-RAY DIFFRACTIONr_chiral_restr0.0810.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02465
X-RAY DIFFRACTIONr_nbd_refined0.2120.2418
X-RAY DIFFRACTIONr_nbd_other0.190.22160
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21108
X-RAY DIFFRACTIONr_nbtor_other0.0820.21429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0621782
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39732377
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23241005
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2195834
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.22 90
Rwork0.172 1617
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)
11.19590.10750.19941.13570.0580.80650.019-0.0201-0.04530.0855-0.02420.02040.0677-0.02580.0052-0.0264-0.00090.0204-0.03790.002-0.05629.58120.70834.924
20.39910.32950.00061.5912-0.37410.10640.05150.1821-0.0544-0.2736-0.1089-0.36830.03090.39980.05740.09380.0283-0.00740.0938-0.0030.099329.19822.36239.78
31.86370.03360.31340.83640.06760.8906-0.02060.10050.0289-0.03550.009-0.02860.02110.02660.0116-0.0661-0.01110.003-0.07860.0077-0.08043.0124.13818.035
44.340.4879-1.40531.4780.38291.4985-0.01860.0394-0.2963-0.0657-0.02820.08340.1008-0.02920.0468-0.0399-0.0046-0.0204-0.0584-0.0058-0.0397-11.84513.7757.887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 93
2X-RAY DIFFRACTION1A130 - 147
3X-RAY DIFFRACTION2A94 - 129
4X-RAY DIFFRACTION3B9 - 93
5X-RAY DIFFRACTION3B130 - 147
6X-RAY DIFFRACTION4B94 - 129

+
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