[English] 日本語
Yorodumi
- PDB-2glz: Crystal structure of a formylmethanofuran dehydrogenase subunit e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2glz
TitleCrystal structure of a formylmethanofuran dehydrogenase subunit e-like protein (dhaf_2992) from desulfitobacterium hafniense dcb-2 at 1.45 A resolution
Componentssimilar to Formylmethanofuran dehydrogenase subunit E
KeywordsMETAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


60s Ribosomal Protein L30; Chain: A; - #130 / Formylmethanofuran dehydrogenase, subunit E domain / FmdE, Molybdenum formylmethanofuran dehydrogenase operon / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / : / Formylmethanofuran dehydrogenase subunit E region
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved alpha+beta core domain and an auxiliary C-terminal treble-clef zinc finger.
Authors: Axelrod, H.L. / Das, D. / Abdubek, P. / Astakhova, T. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C.L. / Feuerhelm, J. ...Authors: Axelrod, H.L. / Das, D. / Abdubek, P. / Astakhova, T. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Lam, W.W. / Marciano, D. / McMullan, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG: MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG: MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: similar to Formylmethanofuran dehydrogenase subunit E
B: similar to Formylmethanofuran dehydrogenase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,52124
Polymers35,1552
Non-polymers1,36522
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-84 kcal/mol
Surface area15870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.425, 84.791, 100.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein similar to Formylmethanofuran dehydrogenase subunit E


Mass: 17577.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / Gene: ZP_01368882.1 / Production host: Escherichia coli (E. coli) / References: GenBank: 68208641, UniProt: B8FYU2*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.8
Details: 0.2M MgCl2, 20.0% PEG-3350, No Buffer, pH 5.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 20, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979051
ReflectionResolution: 1.45→29.894 Å / Num. obs: 71200 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
1.45-1.494.60.72912411251860.72999.9
1.49-1.537.40.6313718250340.6399.9
1.53-1.577.60.4931.53781049650.493100
1.57-1.627.60.37423643747720.374100
1.62-1.677.60.2982.53549446520.298100
1.67-1.737.60.2572.93468045450.257100
1.73-1.87.70.2013.73316043290.201100
1.8-1.877.70.1614.53217941920.161100
1.87-1.967.60.14543051340260.145100
1.96-2.057.70.11162969938770.111100
2.05-2.167.60.10262762136560.102100
2.16-2.297.50.096.52649735160.09100
2.29-2.457.70.0748.12526532910.074100
2.45-2.657.70.0668.82343230590.066100
2.65-2.97.60.05810.42184228560.058100
2.9-3.247.60.05211.51958625740.052100
3.24-3.747.50.0511.61726222870.05100
3.74-4.597.50.04712.91467119680.04799.8
4.59-6.487.30.04512.91122015450.04599.8
6.48-29.896.50.04512.256888700.04594.8

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→27.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.688 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.061
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3). X-RAY ANOMALOUS SCATTERING MEASUREMENTS INDICATE EITHER A ZINC OR A NICKEL CATION ION IS COORDINATED IN AN TETRAHEDERAL COMPLEX TO THE SIDECHAINS OF HIS-15, HIS-17, CYS-19, AND CYS-55. THE RELATIVE OCCUPANCIES OF THE THE METAL IONS WERE ESTIMATED FROM THE RATIO OF THEIR ANOMALOUS DIFFERENCE MAP PEAK HEIGHTS. THE TOTAL OCCUPANCY OF THE ZN AND NI CATIONS WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING OBSERVED AT THIS SITE. 4). SEVERAL MOLECULES OF THE CRYOPROTECTANT, ETHYLENE GLYCOL, WERE MODELED INTO THE STRUCTURE. 5). UNKNOWN DIFFERENCE DENSITY, BETWEEN THE SIDECHAINS OF ASN 64 AND PHE 87 ON BOTH SUBUNITS, IN THE ASYMMETRIC UNIT HAS NOT BEEN MODELED. 6). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3593 5.1 %RANDOM
Rwork0.171 ---
obs0.173 71126 99.86 %-
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: 27.137 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20 Å2
2---1.5 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 76 428 2839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222570
X-RAY DIFFRACTIONr_bond_other_d0.0020.022381
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9663478
X-RAY DIFFRACTIONr_angle_other_deg0.80735541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09223.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20415436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7761517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022834
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02509
X-RAY DIFFRACTIONr_nbd_refined0.210.2502
X-RAY DIFFRACTIONr_nbd_other0.1760.22431
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21216
X-RAY DIFFRACTIONr_nbtor_other0.0860.21477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2305
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0720.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.228
X-RAY DIFFRACTIONr_mcbond_it1.86431590
X-RAY DIFFRACTIONr_mcbond_other0.5033618
X-RAY DIFFRACTIONr_mcangle_it2.6652526
X-RAY DIFFRACTIONr_scbond_it4.32381084
X-RAY DIFFRACTIONr_scangle_it5.66111940
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 260 -
Rwork0.27 4921 -
obs-5181 99.75 %
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)
11.0424-0.194-0.47471.2012-0.14411.5542-0.0072-0.04030.0882-0.00990.0242-0.025-0.10920.0394-0.017-0.2175-0.0050.0019-0.15340.0055-0.119432.87811.87720.712
20.89380.22530.28561.6310.06991.6951-0.04290.0703-0.0403-0.03930.0677-0.03950.06510.0468-0.0248-0.2293-0.0097-0.0026-0.14840.004-0.130634.649-12.23928.211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 151
2X-RAY DIFFRACTION2B4 - 151

+
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://pdbjlc1.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