[English] 日本語
Yorodumi
- PDB-3jzd: Crystal structure of Putative alcohol dehedrogenase (YP_298327.1)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jzd
TitleCrystal structure of Putative alcohol dehedrogenase (YP_298327.1) from RALSTONIA EUTROPHA JMP134 at 2.10 A resolution
ComponentsIron-containing alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / YP_298327.1 / Putative alcohol dehedrogenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


maleylacetate reductase / maleylacetate reductase activity / : / nucleotide binding / metal ion binding
Similarity search - Function
Maleylacetate reductase / Iron-type alcohol dehydrogenase-like / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Maleylacetate reductase / Iron-type alcohol dehydrogenase-like / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Maleylacetate reductase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative alcohol dehedrogenase (YP_298327.1) from RALSTONIA EUTROPHA JMP134 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron-containing alcohol dehydrogenase
B: Iron-containing alcohol dehydrogenase
C: Iron-containing alcohol dehydrogenase
D: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,04825
Polymers150,4744
Non-polymers4,57421
Water15,817878
1
A: Iron-containing alcohol dehydrogenase
B: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,42213
Polymers75,2372
Non-polymers2,18511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-52 kcal/mol
Surface area26440 Å2
MethodPISA
2
C: Iron-containing alcohol dehydrogenase
D: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,62612
Polymers75,2372
Non-polymers2,38910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-54 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.841, 143.841, 169.011
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A4 - 357
2115B4 - 357
3115C4 - 357
4115D4 - 357
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Iron-containing alcohol dehydrogenase


Mass: 37618.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / Gene: Reut_B4129, YP_298327.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46TQ1

-
Non-polymers , 9 types, 899 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 878 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.33 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1900M CaCl2, 5.0000% Glycerol, 26.6000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97833
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97833 Å / Relative weight: 1
ReflectionResolution: 2.1→29.709 Å / Num. obs: 117762 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.926 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.98
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.170.831.56032221196199.3
2.17-2.260.6621.96806423662199.5
2.26-2.360.5322.46412222253199.6
2.36-2.490.4163.16878323826199.6
2.49-2.640.3194.16356321909199.6
2.64-2.850.2395.36804123462199.5
2.85-3.130.15586489822296199.6
3.13-3.590.08313.66757723200199.6
3.59-4.510.04721.86569622514199.4
4.51-29.7090.034286690722839199

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.709 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 8.407 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.145
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.ENDOGENOUS NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON CLEAR ELECTRON DENSITY IN THE EXPERIMENTALLY PHASED DENSITY MODIFIED MAPS. 5.CALCIUM (CA), CHLORIDE (CL) AND PEG FRAGMENTS (PEG, PGE, PG4 AND P6G) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 5902 5 %RANDOM
Rwork0.174 ---
obs0.176 117704 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.77 Å2 / Biso mean: 24.674 Å2 / Biso min: 3.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å20 Å2
2--0.49 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10282 0 295 878 11455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210902
X-RAY DIFFRACTIONr_bond_other_d0.0010.027238
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.99814893
X-RAY DIFFRACTIONr_angle_other_deg0.983317603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.41851448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.77222.289415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.208151552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.93815106
X-RAY DIFFRACTIONr_chiral_restr0.0980.21712
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022142
X-RAY DIFFRACTIONr_mcbond_it1.21327090
X-RAY DIFFRACTIONr_mcbond_other0.24822890
X-RAY DIFFRACTIONr_mcangle_it2.257411268
X-RAY DIFFRACTIONr_scbond_it4.47863812
X-RAY DIFFRACTIONr_scangle_it6.43583607
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2048MEDIUM POSITIONAL0.250.5
2B2048MEDIUM POSITIONAL0.220.5
3C2048MEDIUM POSITIONAL0.180.5
4D2048MEDIUM POSITIONAL0.180.5
1A2070LOOSE POSITIONAL0.475
2B2070LOOSE POSITIONAL0.475
3C2070LOOSE POSITIONAL0.415
4D2070LOOSE POSITIONAL0.445
1A2048MEDIUM THERMAL3.662
2B2048MEDIUM THERMAL2.342
3C2048MEDIUM THERMAL3.472
4D2048MEDIUM THERMAL2.22
1A2070LOOSE THERMAL3.7110
2B2070LOOSE THERMAL3.6410
3C2070LOOSE THERMAL3.6910
4D2070LOOSE THERMAL2.8310
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 456 -
Rwork0.255 8122 -
all-8578 -
obs--99.62 %
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)
10.2847-0.07480.0020.27090.27260.843-0.0119-0.0166-0.00560.02710.0086-0.01090.01390.06060.00330.038-0.01120.00430.02560.01170.01092.003586.034710.5351
20.50640.09510.38730.71450.28160.6501-0.01430.0637-0.0042-0.06730.049-0.0782-0.05140.0724-0.03460.0867-0.01230.02880.0129-0.00450.01686.9061107.4393-19.5602
30.1692-0.12720.08072.08261.02941.30080.0122-0.0158-0.0480.14560.293-0.57130.02280.2954-0.30520.0522-0.0186-0.0280.0926-0.0910.227528.5506135.754815.7847
40.2745-0.29460.18031.80440.06370.40480.0243-0.0519-0.04040.2639-0.00210.19450.1103-0.0727-0.02210.105-0.03970.0290.02450.00020.0357-7.7541133.376422.3043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 357
2X-RAY DIFFRACTION2B4 - 357
3X-RAY DIFFRACTION3C4 - 357
4X-RAY DIFFRACTION4D4 - 357

+
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