[English] 日本語
Yorodumi
- PDB-3meq: Crystal structure of alcohol dehydrogenase from Brucella melitensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3meq
TitleCrystal structure of alcohol dehydrogenase from Brucella melitensis
ComponentsAlcohol dehydrogenase, zinc-containing
KeywordsOXIDOREDUCTASE / structural genomics / infectious disease / Seattle Structural Genomics Center for Infectious Disease / SSGCID / alcohol dehydrogenase / Zinc-binding dehydrogenase
Function / homology
Function and homology information


alcohol dehydrogenase / oxidoreductase activity / nucleotide binding / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / alcohol dehydrogenase / Alcohol dehydrogenase, zinc-containing
Similarity search - Component
Biological speciesBrucella suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsArakaki, T.L. / Staker, B.L. / Gardberg, A. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of alcohol dehydrogenase from Brucella melitensis
Authors: Arakaki, T.L. / Gardberg, A. / Staker, B.L. / Sankaran, B.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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_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: Alcohol dehydrogenase, zinc-containing
B: Alcohol dehydrogenase, zinc-containing
C: Alcohol dehydrogenase, zinc-containing
D: Alcohol dehydrogenase, zinc-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,63433
Polymers154,2964
Non-polymers2,33829
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-200 kcal/mol
Surface area48100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.365, 103.799, 152.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailstetramer

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Alcohol dehydrogenase, zinc-containing


Mass: 38573.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis (bacteria) / Gene: BR0203 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8G2V9, UniProt: A0A0H3G9R2*PLUS

-
Non-polymers , 6 types, 612 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.2 M sodium chloride, 0.1 M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC Q315R / Detector: CCD / Date: Feb 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 94303 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Χ2: 1.02 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.036.30.49145231.01297.1
2.03-2.076.40.46145811.0797.8
2.07-2.116.40.446301.01498.4
2.11-2.156.40.34646231.01598.7
2.15-2.26.50.30546461.03999.1
2.2-2.256.50.27246581.08399.5
2.25-2.316.60.24246751.0699.4
2.31-2.376.70.19446781.04699.7
2.37-2.446.90.17246831.01699.9
2.44-2.5270.15147421.0199.7
2.52-2.617.10.1346731.00599.9
2.61-2.717.30.11547261.07699.9
2.71-2.847.40.09647201.03199.9
2.84-2.997.60.0847201.052100
2.99-3.177.70.07147581.094100
3.17-3.4280.05947541.046100
3.42-3.768.30.05247730.966100
3.76-4.318.60.04848100.948100
4.31-5.438.80.04648670.946100
5.43-508.40.05250630.946100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.63 Å
Translation2.5 Å45.63 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LLU

1llu


Resolution: 2→44.75 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.201 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.204 4713 5 %RANDOM
Rwork0.171 ---
obs0.173 94057 99 %-
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: 28.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9881 0 123 583 10587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210380
X-RAY DIFFRACTIONr_bond_other_d0.0010.026781
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.96614169
X-RAY DIFFRACTIONr_angle_other_deg1.099316651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83151402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6924.519405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.129151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7521553
X-RAY DIFFRACTIONr_chiral_restr0.0850.21635
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021982
X-RAY DIFFRACTIONr_mcbond_it0.5651.56764
X-RAY DIFFRACTIONr_mcbond_other0.1181.52822
X-RAY DIFFRACTIONr_mcangle_it1.038210879
X-RAY DIFFRACTIONr_scbond_it1.85633616
X-RAY DIFFRACTIONr_scangle_it3.0694.53267
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 300 -
Rwork0.206 6197 -
all-6497 -
obs--94.54 %
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)
11.48880.3309-0.17411.6723-0.54980.3141-0.04960.312-0.1035-0.2705-0.0023-0.1764-0.00750.16950.0520.2964-0.04890.02130.366-0.02570.190725.311-22.3865-24.9192
21.57620.12251.04170.91150.57091.5555-0.01530.0797-0.1532-0.01350.04270.01350.036-0.0009-0.02740.2855-0.01990.0130.3011-0.0020.288323.6284-23.7908-11.4488
30.45690.2170.07071.12560.21780.9854-0.00780.10040.0458-0.14990.04680.0955-0.0754-0.0286-0.0390.28730.0118-0.0390.28710.00670.28915.7962-1.2063-13.4074
40.91870.59190.23931.23550.2450.4534-0.04210.14250.1514-0.20190.04510.0408-0.16030.0648-0.0030.3155-0.0114-0.01430.26820.01530.268126.79022.6252-8.934
51.5928-0.2365-0.90561.26560.82761.7792-0.05340.33090.0901-0.4942-0.00310.1264-0.0422-0.12350.05640.398-0.0265-0.06760.30440.03870.194718.1626-9.2342-29.3928
62.7697-0.42520.01380.90060.40991.36580.018-0.3581-0.46070.1947-0.01680.23180.1725-0.1475-0.00120.2508-0.01960.04340.22390.09170.337820.6934-42.436319.1104
71.5617-0.81540.9031.8876-0.25460.89280.03330.1599-0.0631-0.06-0.07260.00770.00120.06490.03930.2886-0.00410.02480.29770.01170.290822.7513-29.55126.6681
80.7438-0.09130.09690.95330.30940.3809-0.0326-0.1005-0.07450.06370.0532-0.00260.0509-0.0024-0.02060.27820.01110.01440.29190.02590.262128.1072-26.363719.8935
91.2389-0.2911-0.46880.71150.49450.8662-0.0268-0.36260.07510.19450.02250.00940.07460.03770.00430.29210.01860.00720.3343-0.0140.222321.719-12.405630.2369
103.35622.04180.17923.9514-0.57571.22520.1011-0.69-0.27820.5073-0.0652-0.07510.1325-0.1985-0.03590.27170.04290.01310.3590.07880.20130.4812-34.914128.651
111.54160.02950.60211.9892-0.5814.2115-0.157-0.40690.32610.21980.08370.1721-0.7001-0.59370.07330.31160.20550.00040.2926-0.13830.33871.475921.758325.3971
124.0336-1.71661.54672.18450.66571.8123-0.029-0.14650.18650.0397-0.0277-0.0883-0.0335-0.10310.05670.28790.02520.03410.2807-0.04940.305616.720911.776222.8414
130.80130.02460.12141.00870.17710.8985-0.0459-0.08130.14940.02490.01840.1417-0.1016-0.1320.02760.25820.0337-0.00580.2801-0.01710.31990.55244.025311.0612
140.82120.09910.1181.701-0.45210.5778-0.0301-0.10590.01020.02570.03650.12940.0229-0.1205-0.00640.24860.01660.01660.288-0.02230.27795.5571-6.008115.069
153.9354-2.50793.82861.8463-1.367413.3489-0.1621-1.0346-0.53820.07290.4840.616-0.3164-2.0762-0.32190.06960.18050.01790.64350.05130.5656-10.859615.155619.496
161.9446-0.00461.13754.9239-1.05550.9463-0.14110.06240.22370.5359-0.0017-1.0787-0.2430.04560.14280.4045-0.1655-0.01460.2213-0.07620.840252.494130.709612.5879
171.4424-0.1131-0.05762.6886-0.37743.0318-0.1054-0.17590.35580.46280.0802-0.2156-0.2211-0.00660.02520.3698-0.0171-0.10510.2099-0.08140.352543.032523.859218.7528
183.13880.28750.58051.66450.12940.7318-0.0727-0.1080.26320.17990.02350.035-0.1435-0.05520.04910.3198-0.0202-0.03570.2316-0.03310.296333.453319.808613.6661
190.6352-0.20120.11410.98380.11010.9379-0.0507-0.03310.04150.07120.0428-0.134-0.03580.10440.00790.265-0.0103-0.01680.2814-0.00490.304744.2309-2.04049.6379
202.02220.42770.8213.7366-4.35656.0119-0.29220.1166-0.28580.1061-0.4506-0.8956-0.23530.61530.74280.18-0.0403-0.20260.23680.00820.674457.128316.73717.7128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 78
2X-RAY DIFFRACTION2A79 - 136
3X-RAY DIFFRACTION3A137 - 218
4X-RAY DIFFRACTION4A219 - 309
5X-RAY DIFFRACTION5A310 - 343
6X-RAY DIFFRACTION6B3 - 77
7X-RAY DIFFRACTION7B78 - 112
8X-RAY DIFFRACTION8B113 - 188
9X-RAY DIFFRACTION9B189 - 302
10X-RAY DIFFRACTION10B303 - 344
11X-RAY DIFFRACTION11C3 - 86
12X-RAY DIFFRACTION12C87 - 112
13X-RAY DIFFRACTION13C113 - 229
14X-RAY DIFFRACTION14C230 - 312
15X-RAY DIFFRACTION15C313 - 343
16X-RAY DIFFRACTION16D3 - 17
17X-RAY DIFFRACTION17D18 - 90
18X-RAY DIFFRACTION18D91 - 134
19X-RAY DIFFRACTION19D135 - 312
20X-RAY DIFFRACTION20D313 - 344

+
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