[English] 日本語
Yorodumi
- PDB-6yk9: [Fe]-hydrogenase from Methanolacinia paynteri with bound guanylyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yk9
Title[Fe]-hydrogenase from Methanolacinia paynteri with bound guanylylpyridinol at 1.7-A resolution
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / [Fe]-hydrogenase / FeGP cofactor / guanylylpyridinol / conformational changes / GMP
Function / homologyGUANOSINE-5'-MONOPHOSPHATE / Chem-FEG / GLYCINE / GUANOSINE
Function and homology information
Biological speciesMethanolacinia paynteri G-2000 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWagner, T. / Huang, G. / Arriaza-Gallardo, F.J. / Shima, S.
Funding support Germany, China, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)Iron sulfur for life SH87/1-1 Germany
Ministry of Education (MoE, China)China Scholarship Council China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.
Authors: Huang, G. / Wagner, T. / Demmer, U. / Warkentin, E. / Ermler, U. / Shima, S.
History
DepositionApr 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5,10-methenyltetrahydromethanopterin hydrogenase
B: 5,10-methenyltetrahydromethanopterin hydrogenase
C: 5,10-methenyltetrahydromethanopterin hydrogenase
E: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,65711
Polymers148,8934
Non-polymers1,7647
Water19,2401068
1
A: 5,10-methenyltetrahydromethanopterin hydrogenase
E: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4096
Polymers74,4462
Non-polymers9634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-84 kcal/mol
Surface area24910 Å2
MethodPISA
2
B: 5,10-methenyltetrahydromethanopterin hydrogenase
C: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2485
Polymers74,4462
Non-polymers8023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-92 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.827, 93.266, 83.642
Angle α, β, γ (deg.)90.000, 97.530, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCE

#1: Protein
5,10-methenyltetrahydromethanopterin hydrogenase /


Mass: 37223.199 Da / Num. of mol.: 4 / Mutation: Wild-type
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Methanolacinia paynteri G-2000 (archaea)
Tissue: / / Cell: / / Cell line: / / Gene: hmd / Organ: / / Variant: DSM 2545
Details (production host): The DNA synthesized was inserted into the expression vector pET-24b (+) at the NdeI and SalI restriction-enzyme digestion-sites
Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): /
References: 5,10-methenyltetrahydromethanopterin hydrogenase

-
Non-polymers , 6 types, 1075 molecules

#2: Chemical ChemComp-FEG / 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine


Mass: 542.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N6O11P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1068 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.42 % / Description: Transparent long orthorhombic rod
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 at 283.15 K using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of ...Details: [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 at 283.15 K using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml reconstituted holoenzyme was mixed with 0.7-ul reservoir solution (from crystallization kits) under yellow light and incubated under dark conditions. The best diffracting crystal came out within two weeks in 25% w/v polyethylene glycol 1500 and 100 mM SPG buffer pH 8.5 (JBScreen Wizard 3&4 HTS, Jena Bioscience). For cryo protection, the crystal was soaked in the crystallization solution supplemented with 10% v/v glycerol.
PH range: 8.5 / Temp details: /

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.7→82.92 Å / Num. obs: 133035 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.065 / Rrim(I) all: 0.125 / Rsym value: 0.107 / Net I/av σ(I): 5.4 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.7-1.793.80.5171.5193980.6050.3080.6030.51799.1
1.79-1.93.80.391.9184260.2330.4550.3999.4
1.9-2.033.80.262.9172380.1550.3040.2699.3
2.03-2.193.80.1814.2160860.1080.2110.18199.3
2.19-2.43.70.1455.2148420.0880.170.14599.4
2.4-2.693.70.1156.4133900.070.1350.11599.2
2.69-3.13.60.0927.6118330.0570.1090.09298.9
3.1-3.83.40.0689.699210.0430.080.06898.6
3.8-5.383.40.0610.176500.0380.0710.0697.8
5.38-46.6333.40.05310.442510.0340.0630.05397.8

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJF

4jjf


Resolution: 1.7→24.89 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.216 6533 4.91 %RANDOM
Rwork0.189 ---
obs0.19 132993 99 %-
Displacement parametersBiso max: 115.74 Å2 / Biso mean: 23.15 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1--3.5604 Å20 Å2-0.6402 Å2
2--1.2428 Å20 Å2
3---2.3176 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.7→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10393 0 114 1068 11575
Biso mean--26.62 29.13 -
Num. residues----1364
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4862SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3317HARMONIC5
X-RAY DIFFRACTIONt_it21660HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1524SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25922SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d21660HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg39526HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion13.51
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 519 5.29 %
Rwork0.2128 9284 -
all0.2147 9803 -
obs--99.18 %
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)
10.2001-0.0506-0.05630.59870.10180.6042-0.00110.01250.00820.0867-0.0070.0426-0.0269-0.02510.0081-0.0271-0.00060.0143-0.06950.0204-0.01084.5015-5.4533102.0731
20.33640.0186-0.0810.19540.11581.038-0.01630.038-0.0037-0.0414-0.01170.01180.0175-0.02220.028-0.02540.00220.0349-0.07270.0185-0.003310.10824.000971.6947
30.1120.0518-0.1710.90350.05511.1890.05340.00050.0060.1264-0.00260.0278-0.2372-0.0213-0.05090.0235-0.00070.0478-0.08740.0195-0.05917.374441.9201107.2947
40.1001-0.1277-0.01690.44860.00421.1651-0.00350.0030.0068-0.1221-0.0304-0.03620.13270.04510.0340.02570.00450.0611-0.07810.0284-0.040512.417-23.265367.2903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 342
2X-RAY DIFFRACTION2{ B|* }B2 - 342
3X-RAY DIFFRACTION3{ C|* }C2 - 342
4X-RAY DIFFRACTION4{ E|* }E2 - 342

+
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