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- PDB-4h73: Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexe... -

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Basic information

Entry
Database: PDB / ID: 4h73
TitleThermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Fold / protein / aldehyde oxidation / NADP reduction / Intracellular / cytoplasmic
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / NICKEL (II) ION / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesPyrobaculum sp. (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPetrova, T. / Shabalin, I.G. / Bezsudnova, E.Y. / Boyko, K.M. / Mardanov, A.V. / Gumerov, V.M. / Ravin, N.V. / Popov, V.O.
CitationJournal: To be Published
Title: Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+
Authors: Petrova, T. / Shabalin, I.G. / Bezsudnova, E.Y. / Boyko, K.M. / Mardanov, A.V. / M Gumerov, V. / Ravin, N.V. / Popov, V.O.
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_label_asym_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_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.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_conn.ptnr2_label_seq_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: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,87220
Polymers435,6748
Non-polymers6,19812
Water27,1491507
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4685
Polymers108,9182
Non-polymers1,5503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-38 kcal/mol
Surface area34120 Å2
MethodPISA
2
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4685
Polymers108,9182
Non-polymers1,5503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-38 kcal/mol
Surface area34220 Å2
MethodPISA
3
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4685
Polymers108,9182
Non-polymers1,5503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-37 kcal/mol
Surface area34260 Å2
MethodPISA
4
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4685
Polymers108,9182
Non-polymers1,5503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-40 kcal/mol
Surface area34300 Å2
MethodPISA
5
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,93610
Polymers217,8374
Non-polymers3,0996
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25650 Å2
ΔGint-79 kcal/mol
Surface area60320 Å2
MethodPISA
6
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,93610
Polymers217,8374
Non-polymers3,0996
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25780 Å2
ΔGint-80 kcal/mol
Surface area60450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.210, 183.770, 206.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Aldehyde dehydrogenase /


Mass: 54459.207 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: The gene P186_1147 encoding the aldehyde dehydrogenase was cloned into the expression vector pQE60 (Qiagen) at NcoI/HindIII sites. Due to introduction of the NcoI cloning site the ...Details: The gene P186_1147 encoding the aldehyde dehydrogenase was cloned into the expression vector pQE60 (Qiagen) at NcoI/HindIII sites. Due to introduction of the NcoI cloning site the recombinant protein contains valine instead of isoleucine after the first methionine.
Source: (gene. exp.) Pyrobaculum sp. (archaea) / Strain: 1860 / Gene: P186_1147 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): DLT1270/pRARE2 / References: UniProt: G7VCG0
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1507 / 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: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.01 M Nickel(II) chloride hexahydrate, 0.1 M Tris pH 8.5, 1.0 M Lithium sulfate monohydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9815 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 20, 2011
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9815 Å / Relative weight: 1
ReflectionResolution: 2.4→164.21 Å / Num. all: 667272 / Num. obs: 228986 / % possible obs: 94 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.98 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.282 / Net I/σ(I): 8.36
Reflection shellResolution: 2.4→2.54 Å / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.64 / Num. unique all: 35519 / % possible all: 94.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.625 Å / SU ML: 0.79 / σ(F): 1.34 / Phase error: 32.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 11476 5.01 %Random
Rwork0.2121 ---
obs0.2146 228869 94.28 %-
all-228869 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.691 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.2897 Å2-0 Å2-0 Å2
2---8.5411 Å20 Å2
3----5.7486 Å2
Refine analyzeLuzzati coordinate error obs: 0.79 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30084 0 252 1507 31843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00830979
X-RAY DIFFRACTIONf_angle_d1.26542052
X-RAY DIFFRACTIONf_dihedral_angle_d16.62111304
X-RAY DIFFRACTIONf_chiral_restr0.0954728
X-RAY DIFFRACTIONf_plane_restr0.0065394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.39763400.34326604X-RAY DIFFRACTION87
2.4273-2.45580.38193820.32767342X-RAY DIFFRACTION96
2.4558-2.48580.36623900.31277374X-RAY DIFFRACTION96
2.4858-2.51720.36873920.30157322X-RAY DIFFRACTION96
2.5172-2.55030.3343690.27877354X-RAY DIFFRACTION97
2.5503-2.58520.32433910.27067404X-RAY DIFFRACTION97
2.5852-2.62210.33224150.26637295X-RAY DIFFRACTION96
2.6221-2.66130.32073770.25387375X-RAY DIFFRACTION96
2.6613-2.70280.32863780.27137398X-RAY DIFFRACTION96
2.7028-2.74710.31693740.25327356X-RAY DIFFRACTION96
2.7471-2.79440.32663860.25887379X-RAY DIFFRACTION96
2.7944-2.84520.29833770.24117375X-RAY DIFFRACTION96
2.8452-2.89990.28283840.23077353X-RAY DIFFRACTION96
2.8999-2.9590.29284040.23587308X-RAY DIFFRACTION96
2.959-3.02330.28873800.23277365X-RAY DIFFRACTION96
3.0233-3.09360.28673930.23357329X-RAY DIFFRACTION96
3.0936-3.17080.32224030.23187300X-RAY DIFFRACTION96
3.1708-3.25650.27084090.22727259X-RAY DIFFRACTION95
3.2565-3.35220.27193720.21377321X-RAY DIFFRACTION95
3.3522-3.46020.27514070.21277227X-RAY DIFFRACTION95
3.4602-3.58370.24864170.20637193X-RAY DIFFRACTION94
3.5837-3.72690.23563870.2027224X-RAY DIFFRACTION94
3.7269-3.89620.21633720.18867205X-RAY DIFFRACTION93
3.8962-4.10110.23493890.17737117X-RAY DIFFRACTION93
4.1011-4.35730.2153970.16257089X-RAY DIFFRACTION92
4.3573-4.69250.18863580.15027105X-RAY DIFFRACTION91
4.6925-5.16250.20523470.1597125X-RAY DIFFRACTION91
5.1625-5.90430.23123590.19227150X-RAY DIFFRACTION91
5.9043-7.41950.23243710.19227142X-RAY DIFFRACTION91
7.4195-29.62740.18733560.17737003X-RAY DIFFRACTION86

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