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- PDB-4jbi: 2.35A resolution structure of NADPH bound thermostable alcohol de... -

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Basic information

Entry
Database: PDB / ID: 4jbi
Title2.35A resolution structure of NADPH bound thermostable alcohol dehydrogenase from Pyrobaculum aerophilum
ComponentsAlcohol dehydrogenase (Zinc)
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / thermostability / Zinc binding / NADPH
Function / homology
Function and homology information


anion binding / adenyl nucleotide binding / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / protein tetramerization / metal ion binding
Similarity search - Function
: / 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 ...: / 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
Chem-NDP / Alcohol dehydrogenase (Zinc)
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsLovell, S. / Battaile, K.P. / Vitale, A. / Throne, N. / Hu, X. / Shen, M. / D'Auria, S. / Auld, D.S.
CitationJournal: Plos One / Year: 2013
Title: Physicochemical Characterization of a Thermostable Alcohol Dehydrogenase from Pyrobaculum aerophilum.
Authors: Vitale, A. / Thorne, N. / Lovell, S. / Battaile, K.P. / Hu, X. / Shen, M. / D'Auria, S. / Auld, D.S.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 22, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop ...pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_struct_assembly_prop.value / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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)
B: Alcohol dehydrogenase (Zinc)
C: Alcohol dehydrogenase (Zinc)
D: Alcohol dehydrogenase (Zinc)
E: Alcohol dehydrogenase (Zinc)
F: Alcohol dehydrogenase (Zinc)
G: Alcohol dehydrogenase (Zinc)
H: Alcohol dehydrogenase (Zinc)
I: Alcohol dehydrogenase (Zinc)
J: Alcohol dehydrogenase (Zinc)
K: Alcohol dehydrogenase (Zinc)
L: Alcohol dehydrogenase (Zinc)
M: Alcohol dehydrogenase (Zinc)
N: Alcohol dehydrogenase (Zinc)
O: Alcohol dehydrogenase (Zinc)
P: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)631,98648
Polymers619,01316
Non-polymers12,97332
Water19,9431107
1
A: Alcohol dehydrogenase (Zinc)
E: Alcohol dehydrogenase (Zinc)
F: Alcohol dehydrogenase (Zinc)
K: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99612
Polymers154,7534
Non-polymers3,2438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-49 kcal/mol
Surface area46320 Å2
MethodPISA
2
B: Alcohol dehydrogenase (Zinc)
C: Alcohol dehydrogenase (Zinc)
D: Alcohol dehydrogenase (Zinc)
L: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99612
Polymers154,7534
Non-polymers3,2438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-51 kcal/mol
Surface area46470 Å2
MethodPISA
3
G: Alcohol dehydrogenase (Zinc)
H: Alcohol dehydrogenase (Zinc)
N: Alcohol dehydrogenase (Zinc)
P: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99612
Polymers154,7534
Non-polymers3,2438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-49 kcal/mol
Surface area46060 Å2
MethodPISA
4
I: Alcohol dehydrogenase (Zinc)
J: Alcohol dehydrogenase (Zinc)
M: Alcohol dehydrogenase (Zinc)
O: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,99612
Polymers154,7534
Non-polymers3,2438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-51 kcal/mol
Surface area45980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.133, 169.262, 149.151
Angle α, β, γ (deg.)90.000, 116.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alcohol dehydrogenase (Zinc)


Mass: 38688.293 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea)
Strain: ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827
Gene: PAE2687 / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q8ZUP0, alcohol dehydrogenase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1107 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10%(w/v) PEG 8000, 100 mM Hepes, 8% (v/v) ethylene glycol, pH 7.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→133.767 Å / Num. all: 254725 / Num. obs: 254725 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.7 / Num. unique all: 12550 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHASERphasing
PHENIXdev_1241refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JBG

4jbg


Resolution: 2.35→44.589 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 12800 5.03 %RANDOM
Rwork0.1613 ---
obs0.1639 254638 99.89 %-
all-254638 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.66 Å2 / Biso mean: 43.351 Å2 / Biso min: 18.54 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38810 0 784 1107 40701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01140503
X-RAY DIFFRACTIONf_angle_d1.17255353
X-RAY DIFFRACTIONf_chiral_restr0.0766414
X-RAY DIFFRACTIONf_plane_restr0.0077112
X-RAY DIFFRACTIONf_dihedral_angle_d15.68214661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.37670.31563740.236380908464100
2.3767-2.40470.27183810.215580448425100
2.4047-2.4340.30954330.217280528485100
2.434-2.46480.26754420.209479998441100
2.4648-2.49720.27124380.208680548492100
2.4972-2.53140.28294250.205580708495100
2.5314-2.56760.27534380.201780268464100
2.5676-2.60590.28033970.190180688465100
2.6059-2.64660.27224410.191380248465100
2.6466-2.690.25514480.177979828430100
2.69-2.73640.24344370.172280338470100
2.7364-2.78610.23613910.170980948485100
2.7861-2.83970.23914530.176480368489100
2.8397-2.89770.25554860.182379858471100
2.8977-2.96070.25544210.178880588479100
2.9607-3.02950.25743950.182381008495100
3.0295-3.10530.23084270.173780468473100
3.1053-3.18920.23184400.172380508490100
3.1892-3.2830.23774400.170180318471100
3.283-3.3890.24524490.178680808529100
3.389-3.510.23034240.179180038427100
3.51-3.65050.23334340.169180708504100
3.6505-3.81660.20844220.170781108532100
3.8166-4.01770.19314220.148880708492100
4.0177-4.26920.18174160.133980708486100
4.2692-4.59850.15593980.121681108508100
4.5985-5.06070.14884260.11681008526100
5.0607-5.79160.15064270.124781258552100
5.7916-7.29170.17314260.132781248550100
7.2917-44.59710.14674490.13358134858399

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