[English] 日本語
Yorodumi
- PDB-4pya: MoaC K51A in complex with 3',8-cH2GTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pya
TitleMoaC K51A in complex with 3',8-cH2GTP
ComponentsMolybdenum cofactor biosynthesis protein MoaC
KeywordsTRANSLATION / MoaC / Molybdenum Cofactor / Moco
Function / homology
Function and homology information


cyclic pyranopterin monophosphate synthase / cyclic pyranopterin monophosphate synthase activity / Mo-molybdopterin cofactor biosynthetic process / protein-containing complex / identical protein binding
Similarity search - Function
: / Molybdopterin cofactor biosynthesis C (MoaC) domain / Molybdopterin cofactor biosynthesis C (MoaC) domain / Molybdenum cofactor biosynthesis C / Molybdopterin cofactor biosynthesis C (MoaC) domain superfamily / MoaC family / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2X3 / Cyclic pyranopterin monophosphate synthase / :
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å
AuthorsTonthat, N.K. / Hover, B.M. / Yokoyama, K. / Schumacher, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis.
Authors: Hover, B.M. / Tonthat, N.K. / Schumacher, M.A. / Yokoyama, K.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Aug 29, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein MoaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3779
Polymers17,4191
Non-polymers9588
Water93752
1
A: Molybdenum cofactor biosynthesis protein MoaC
hetero molecules

A: Molybdenum cofactor biosynthesis protein MoaC
hetero molecules

A: Molybdenum cofactor biosynthesis protein MoaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,13027
Polymers52,2583
Non-polymers2,87324
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area2670 Å2
ΔGint-15 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.933, 89.933, 62.446
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-206-

EDO

-
Components

#1: Protein Molybdenum cofactor biosynthesis protein MoaC


Mass: 17419.174 Da / Num. of mol.: 1 / Fragment: MoaC / Mutation: K51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: W0KCK5, UniProt: P0A738*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-2X3 / (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 35% PEG 1500 and 0.1 M MMT buffer (pH 9.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.789→50 Å / Num. all: 14516 / Num. obs: 14516 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 34.04 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.863 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.825.60.6756890.993199.6
1.82-1.856.60.5967200.971199.4
1.85-1.896.90.4597100.9871100
1.89-1.937.10.3826950.995199.9
1.93-1.977.10.2937111.0891100
1.97-2.027.10.2197191.0831100
2.02-2.077.10.1877161.121100
2.07-2.127.10.1527011.1921100
2.12-2.187.10.1337281.2811100
2.18-2.267.10.1167171.463199.9
2.26-2.347.10.1027241.6431100
2.34-2.437.10.0877181.8261100
2.43-2.5470.0817192.081100
2.54-2.6770.0677292.1631100
2.67-2.846.90.0617272.3481100
2.84-3.066.80.067372.7181100
3.06-3.376.60.0597333.423199.7
3.37-3.866.40.057473.441199.3
3.86-4.866.30.0467633.342199.3
4.86-505.60.0448133.329196.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID: 1EKR

1ekr


Resolution: 1.789→29.437 Å / FOM work R set: 0.8577 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 1450 10 %RANDOM
Rwork0.1738 ---
all0.1758 14505 --
obs0.1758 14505 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.39 Å2 / Biso mean: 47.36 Å2 / Biso min: 24.94 Å2
Refinement stepCycle: LAST / Resolution: 1.789→29.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 60 52 1061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091017
X-RAY DIFFRACTIONf_angle_d1.4081373
X-RAY DIFFRACTIONf_chiral_restr0.102167
X-RAY DIFFRACTIONf_plane_restr0.009167
X-RAY DIFFRACTIONf_dihedral_angle_d16.998427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7891-1.85310.29711390.24751258139799
1.8531-1.92730.24191420.214412651407100
1.9273-2.0150.20071420.187312841426100
2.015-2.12120.20861430.174812801423100
2.1212-2.2540.23461430.178912961439100
2.254-2.4280.21961450.181213041449100
2.428-2.67220.21921440.184412971441100
2.6722-3.05850.19151470.177513181465100
3.0585-3.8520.19311480.175313341482100
3.852-29.44150.16651570.15861419157698
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)
16.8108-0.2165-4.34083.63471.01746.56640.01760.53020.0036-0.1451-0.11840.3785-0.2105-0.46840.04410.20010.0504-0.07360.33360.01210.2497-70.106223.79199.6618
25.9249-0.5407-6.88820.59020.95628.2084-0.6856-0.22823.94520.12610.95761.9872-3.8283-3.4782-0.05731.27350.4213-0.04950.9330.06891.3019-71.008837.803206.1517
34.8398-5.3859-2.22239.06952.29414.49010.00120.1310.4155-0.18450.0251-0.6727-0.12460.30170.00990.277-0.0661-0.00680.2837-0.00380.3125-54.611624.3834196.428
49.29716.1691-3.44614.9542-4.2865.8425-0.65841.91520.3665-0.510.61940.40950.2065-1.73090.02380.42720.0209-0.01850.468-0.02150.3977-72.409926.2113197.0093
55.3033-0.9656-3.28712.77540.41288.4374-0.03460.35080.051-0.1992-0.0110.1614-0.0102-0.12780.06350.16960.0004-0.01640.2078-0.02260.242-65.062120.6636199.5754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 47 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 53 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 82 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 94 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 146 )A0

+
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