[English] 日本語
Yorodumi
- PDB-2nqr: MoeA D142N -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nqr
TitleMoeA D142N
ComponentsMolybdopterin biosynthesis protein moeA
KeywordsBIOSYNTHETIC PROTEIN / molybdopterin / MPT / Moco / molybdenum / MoeA / MogA / gephyrin / Cnx1 / cinnamon
Function / homology
Function and homology information


molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / Mo-molybdopterin cofactor biosynthetic process / protein homodimerization activity / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 2. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily ...Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 2. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Molybdopterin molybdenumtransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNicolas, J. / Xiang, S. / Schindelin, H. / Rajagopalan, K.V.
CitationJournal: Biochemistry / Year: 2007
Title: Mutational Analysis of Escherichia coli MoeA: Two Functional Activities Map to the Active Site Cleft.
Authors: Nichols, J.D. / Xiang, S. / Schindelin, H. / Rajagopalan, K.V.
History
DepositionOct 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Molybdopterin biosynthesis protein moeA
B: Molybdopterin biosynthesis protein moeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,86820
Polymers88,2102
Non-polymers1,65818
Water15,115839
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-41 kcal/mol
Surface area33450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.284, 100.076, 102.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer of chains A and B

-
Components

#1: Protein Molybdopterin biosynthesis protein moeA


Mass: 44105.074 Da / Num. of mol.: 2 / Mutation: D142N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: moeA, bisB, chlE, narE / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): AH69 (DE3) / References: UniProt: P12281
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10%-15% PEG 6000/8000, 0.2-0.5 M calcium acetate, 0.1 M cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 37995 / Num. obs: 37554 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.64 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.279 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1981 5 %RANDOM
Rwork0.162 ---
all0.166 37995 --
obs0.166 37554 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 108 839 7031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216294
X-RAY DIFFRACTIONr_bond_other_d0.0030.025851
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9758521
X-RAY DIFFRACTIONr_angle_other_deg0.969313597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855805
X-RAY DIFFRACTIONr_chiral_restr0.1180.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027019
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021229
X-RAY DIFFRACTIONr_nbd_refined0.2320.21371
X-RAY DIFFRACTIONr_nbd_other0.2650.27145
X-RAY DIFFRACTIONr_nbtor_other0.0930.24066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2585
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.246
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.244
X-RAY DIFFRACTIONr_mcbond_it0.981.54000
X-RAY DIFFRACTIONr_mcangle_it1.82426429
X-RAY DIFFRACTIONr_scbond_it3.04732294
X-RAY DIFFRACTIONr_scangle_it5.1354.52092
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.274 120
Rwork0.205 2757
obs-2877
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)
11.14040.5344-0.38220.7376-0.1040.380.0921-0.11470.04570.0139-0.05240.0411-0.0010.0449-0.03980.0276-0.01370.00710.02710.00070.002823.110291.96963.2129
20.45270.07990.06221.50850.17860.4968-0.03850.0658-0.01650.02870.0733-0.0640.0387-0.0121-0.03470.0167-0.0053-0.00690.0112-0.00170.019822.65224.631328.3296
30.0850.03020.00910.2219-0.01580.0213-0.01290.02030.0035-0.00220.0137-0.01510.00920.0084-0.00080.0195-0.001-0.00160.0265-0.00160.011919.344848.570817.2192
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA53 - 14053 - 140
22BB53 - 14053 - 140
33AA7 - 527 - 52
43BB7 - 527 - 52
53AA141 - 410141 - 410
63BB141 - 409141 - 409

+
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