[English] 日本語
Yorodumi
- PDB-2iz5: FUNCTION AND STRUCTURE OF THE MOLYBDENUM COFACTOR CARRIER PROTEIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iz5
TitleFUNCTION AND STRUCTURE OF THE MOLYBDENUM COFACTOR CARRIER PROTEIN MCP FROM CHLAMYDOMONAS REINHARDTII
ComponentsMOCO CARRIER PROTEIN
KeywordsMETAL TRANSPORT
Function / homologySLOG cluster4 / SLOG cluster4 family / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Molybdenum cofactor carrier protein
Function and homology information
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsFischer, K. / Llamas, A. / Tejada-Jimenez, M. / Schrader, N. / Kuper, J. / Mendel, R.R. / Fernandez, E. / Schwarz, G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Function and Structure of the Molybdenum Cofactor Carrier Protein from Chlamydomonas Reinhardtii.
Authors: Fischer, K. / Llamas, A. / Tejada-Jimenez, M. / Schrader, N. / Kuper, J. / Ataya, F.S. / Galvan, A. / Mendel, R.R. / Fernandez, E. / Schwarz, G.
History
DepositionJul 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MOCO CARRIER PROTEIN
B: MOCO CARRIER PROTEIN
C: MOCO CARRIER PROTEIN
D: MOCO CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)71,5554
Polymers71,5554
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-62.5 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.313, 75.881, 126.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
MOCO CARRIER PROTEIN


Mass: 17888.670 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): DL41 / References: UniProt: Q8RV61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.5 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 8 / Details: pH 8.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97962
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 53717 / % possible obs: 94.5 % / Observed criterion σ(I): 2.1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.6
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 88.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.29→65.09 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.408 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS ARE PARTIALLY TRACED WITH ALA RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1471 5.1 %RANDOM
Rwork0.215 ---
obs0.218 27469 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--2.77 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.29→65.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4455 0 0 163 4618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224504
X-RAY DIFFRACTIONr_bond_other_d0.0010.024432
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9876108
X-RAY DIFFRACTIONr_angle_other_deg0.954310291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7735630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29126.29124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73515745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6331511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025019
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02728
X-RAY DIFFRACTIONr_nbd_refined0.2410.21092
X-RAY DIFFRACTIONr_nbd_other0.1920.24475
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22085
X-RAY DIFFRACTIONr_nbtor_other0.090.22918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1221.53966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34124953
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.00931487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0914.51155
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: 2.29→2.35 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 84
Rwork0.248 1602
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)
14.291-0.72541.36093.9572-0.82965.0731-0.1671-0.03290.36810.4158-0.2202-0.0043-0.20530.00620.3873-0.06470.03520.1169-0.1571-0.0494-0.204819.44174.76222.3764
24.22981.23460.17414.65480.42583.4261-0.13980.0402-0.4606-0.0207-0.0115-0.05860.37460.29460.1513-0.0395-0.0096-0.0454-0.0552-0.0035-0.164123.7268-8.5335-14.6709
32.69130.516-1.17311.2224-0.49363.0072-0.0299-0.26070.1375-0.02320.00820.3701-0.0233-0.06020.0217-0.1173-0.005-0.0639-0.0685-0.0348-0.054117.8522-1.1552-7.6211
43.41430.81470.4315.6506-0.73593.3224-0.0803-0.03890.6351-0.1085-0.17760.1294-0.3576-0.20510.2579-0.0766-0.02440.0542-0.0892-0.0229-0.132445.74088.3076-14.109
52.95610.77571.16442.2640.09463.60340.0548-0.1657-0.007-0.045-0.0523-0.2990.08290.0179-0.0026-0.11890.01580.0203-0.03940.0022-0.089650.30041.6472-6.425
65.2802-1.042-1.35083.7785-0.1643.279-0.3244-0.2108-0.4710.51220.04760.23730.11840.0720.27680.01010.1101-0.0378-0.07590.0511-0.149347.0958-4.457423.4002
75.0106-0.6708-1.8112.970.34593.2788-0.00550.06960.27670.08250.1546-0.1931-0.0096-0.0131-0.1491-0.1270.0361-0.0968-0.06930.02-0.199749.61453.716915.6829
83.7388-0.462.56662.15720.81183.68650.01660.2089-0.02860.097-0.04060.25440.1798-0.040.024-0.116-0.03090.1324-0.0702-0.0481-0.130517.9783-3.310814.5072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D5 - 69
2X-RAY DIFFRACTION2A4 - 73
3X-RAY DIFFRACTION3A76 - 166
4X-RAY DIFFRACTION4B1 - 71
5X-RAY DIFFRACTION5B74 - 166
6X-RAY DIFFRACTION6C4 - 69
7X-RAY DIFFRACTION7C75 - 166
8X-RAY DIFFRACTION8D73 - 166

+
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