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- PDB-3meq: Crystal structure of alcohol dehydrogenase from Brucella melitensis -

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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


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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / 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, zinc-containing / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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 / 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 / Nicotinamide adenine dinucleotide


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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