[English] 日本語
Yorodumi
- PDB-2npn: Crystal structure of putative cobalamin synthesis related protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2npn
TitleCrystal structure of putative cobalamin synthesis related protein (CobF) from Corynebacterium diphtheriae
ComponentsPutative cobalamin synthesis related protein
KeywordsTRANSFERASE / cobalamin synthesis related protein / CobF / PSI-2 / MAD / structural genomics / SAM / S-ADENOSYLMETHIONINE / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


precorrin-6A synthase (deacetylating) activity / cobalamin biosynthetic process / methylation / metal ion binding
Similarity search - Function
Precorrin-6A synthase [deacetylating] / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily ...Precorrin-6A synthase [deacetylating] / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Putative cobalamin synthesis related protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsNocek, B. / Zhou, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of cobalamin synthesis related protein (CobF) from Corynebacterium diphtheriae
Authors: Nocek, B. / Zhou, M. / Clancy, S. / Joachimiak, A.
History
DepositionOct 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THIS PROTEIN IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative cobalamin synthesis related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1024
Polymers28,5881
Non-polymers5153
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative cobalamin synthesis related protein
hetero molecules

A: Putative cobalamin synthesis related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2058
Polymers57,1752
Non-polymers1,0306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4110 Å2
ΔGint-20 kcal/mol
Surface area21020 Å2
MethodPISA, PQS
3
A: Putative cobalamin synthesis related protein
hetero molecules

A: Putative cobalamin synthesis related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2058
Polymers57,1752
Non-polymers1,0306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area1320 Å2
ΔGint-16 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.104, 80.845, 76.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-251-

MG

-
Components

#1: Protein Putative cobalamin synthesis related protein


Mass: 28587.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6NIF5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5M Ammonium Chloride, 0.1 M Sodium Acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791, 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2006 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97921
ReflectionResolution: 1.6→30 Å / Num. all: 33440 / Num. obs: 33406 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.899 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19776 1613 5.1 %RANDOM
Rwork0.17197 ---
obs0.17327 30151 99.05 %-
all-31814 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.009 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--0.4 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 34 213 2132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212071
X-RAY DIFFRACTIONr_bond_other_d0.0050.021379
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9612832
X-RAY DIFFRACTIONr_angle_other_deg0.91933364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7025262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2523.22996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.061519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022321
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02419
X-RAY DIFFRACTIONr_nbd_refined0.2040.2424
X-RAY DIFFRACTIONr_nbd_other0.2060.21392
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2993
X-RAY DIFFRACTIONr_nbtor_other0.0840.21078
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.141.51552
X-RAY DIFFRACTIONr_mcbond_other0.2681.5509
X-RAY DIFFRACTIONr_mcangle_it1.35222033
X-RAY DIFFRACTIONr_scbond_it2.2683919
X-RAY DIFFRACTIONr_scangle_it3.254.5794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 94 -
Rwork0.224 2251 -
obs--99.58 %
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)
14.2887-2.56986.51664.5365-7.886217.4142-0.32750.22170.2240.07990.04270.0949-0.5854-0.03350.28490.0475-0.0171-0.07930.0282-0.00050.150.011742.146520.5835
23.0487-1.27891.72653.1937-1.23756.6795-0.1081-0.0675-0.0132-0.0564-0.05810.29760.1523-0.37750.1662-0.0179-0.02390.00940.0498-0.0350.16646.019337.748533.4556
35.54660.5080.12125.3724-3.6415.67770.1156-0.0443-0.8763-0.3071-0.2578-0.00120.57930.32210.14220.0526-0.0062-0.03780.0132-0.02480.145250.455825.878826.8384
48.2552.3457-4.84715.265-1.473710.85980.19640.3720.1399-0.31960.11820.6141-0.0826-0.3452-0.3146-0.0112-0.0069-0.0837-0.0350.00830.149745.368129.199324.0992
529.1433-13.57140.168210.807-0.30193.48530.23881.2579-1.2114-0.5255-0.28750.11210.17080.62460.0487-0.0230.026-0.01230.1534-0.16070.023461.52328.61189.9849
63.0541-0.14332.26220.5515-0.44662.46250.04450.2787-0.0832-0.12060.02130.14230.02760.1228-0.06580.0574-0.0024-0.04970.064-0.00230.07953.108136.987120.8267
77.4291-4.24917.66336.5058-3.470919.6929-0.33930.81090.2448-0.2533-0.0032-0.2866-0.46930.77020.34250.0479-0.0626-0.04220.16360.0082-0.006660.400939.83514.1505
81.9314-0.28341.51744.2447-5.169317.5178-0.35080.18170.1802-0.25950.18150.1559-0.6116-0.22740.16940.0754-0.0528-0.08430.04290.03420.098353.322244.566523.7259
92.6636-1.33822.69474.4173-0.82429.24760.08950.021-0.05110.0454-0.00990.1901-0.06250.0209-0.07960.03640.01840.01230.0571-0.00020.091560.162533.752243.3138
102.19830.4235-0.38842.09140.03361.40630.0234-0.0143-0.0225-0.0025-0.0261-0.0011-0.07280.14690.00270.08530.0146-0.01450.09490.00940.051771.844736.185243.3276
115.2376-0.3065-0.93662.9502-0.59184.410.02610.0551-0.0020.0062-0.0777-0.2965-0.06030.39820.05160.0503-0.0051-0.01450.10750.01410.042479.595636.176542.9279
121.9693-0.30750.37031.74330.15481.52760.0959-0.0399-0.26390.0503-0.02570.10620.18880.082-0.07020.08340.016-0.01240.05210.00520.077169.083624.676745.6993
138.16152.05444.30996.83530.6462.32970.1718-0.2217-0.5460.21-0.10760.02660.4262-0.0964-0.06420.10020.0387-0.00810.01140.010.106169.257716.127345.325
1421.0111-4.478511.672924.26611.406322.86040.5551-0.2714-0.9504-0.42950.17140.85980.8482-0.187-0.72640.2353-0.0023-0.11090.0668-0.06440.263162.226513.182836.4234
151.85010.51550.61062.77020.22151.7159-0.03170.0145-0.1143-0.12140.00710.0951-0.00240.10950.02460.09050.01410.00140.09930.00890.07769.55328.423343.9109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 101 - 11
2X-RAY DIFFRACTION2AA11 - 2812 - 29
3X-RAY DIFFRACTION3AA29 - 4930 - 50
4X-RAY DIFFRACTION4AA50 - 6551 - 66
5X-RAY DIFFRACTION5AA76 - 9377 - 94
6X-RAY DIFFRACTION6AA94 - 11995 - 120
7X-RAY DIFFRACTION7AA120 - 131121 - 132
8X-RAY DIFFRACTION8AA132 - 141133 - 142
9X-RAY DIFFRACTION9AA142 - 150143 - 151
10X-RAY DIFFRACTION10AA151 - 171152 - 172
11X-RAY DIFFRACTION11AA172 - 182173 - 183
12X-RAY DIFFRACTION12AA183 - 220184 - 221
13X-RAY DIFFRACTION13AA221 - 233222 - 234
14X-RAY DIFFRACTION14AA234 - 238235 - 239
15X-RAY DIFFRACTION15AA239 - 250240 - 251

+
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