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- PDB-1o2d: Crystal structure of Alcohol dehydrogenase, iron-containing (TM09... -

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Basic information

Entry
Database: PDB / ID: 1o2d
TitleCrystal structure of Alcohol dehydrogenase, iron-containing (TM0920) from Thermotoga maritima at 1.30 A resolution
ComponentsAlcohol dehydrogenase, iron-containing
KeywordsOXIDOREDUCTASE / TM0920 / ALCOHOL DEHYDROGENASE / IRON-CONTAINING / STRUCTURAL GENOMICS / JCSG / PSI / PROTEIN STRUCTURE INITIATIVE / JOINT CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / nucleotide binding / metal ion binding
Similarity search - Function
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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Alcohol dehydrogenase, iron-containing
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution
Authors: Schwarzenbacher, R. / von Delft, F. / Canaves, J.M. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshaghi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Guda, C. ...Authors: Schwarzenbacher, R. / von Delft, F. / Canaves, J.M. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshaghi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Guda, C. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McMullan, D. / McPhillips, T.M. / Miller, M.A. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Robb, A. / Rodrigues, K. / Selby, T.L. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionJun 10, 2003ID: 1J5R
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 1 .. 900 B 1 .. 900 0.620 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK: NULL

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase, iron-containing
B: Alcohol dehydrogenase, iron-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7278
Polymers83,8852
Non-polymers1,8436
Water16,069892
1
A: Alcohol dehydrogenase, iron-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8644
Polymers41,9421
Non-polymers9213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alcohol dehydrogenase, iron-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8644
Polymers41,9421
Non-polymers9213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.047, 85.283, 72.080
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92814, 0.2932, -0.22933), (-0.28917, -0.95588, -0.05173), (-0.23438, 0.0183, 0.97197)
Vector: 42.86662, 48.62051, 24.52695)

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Components

#1: Protein Alcohol dehydrogenase, iron-containing /


Mass: 41942.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0920 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X022, alcohol dehydrogenase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 1.92 Å3/Da / Density % sol: 35.36 %
Crystal growTemperature: 277 K / pH: 8.7
Details: 20% PEG-300, 10% glycerol, 0.1M Tris pH 8.5 5% (w/v) PEG-8000, pH 8.7, VAPOR DIFFUSION,SITTING DROP,NANODROP, pH 8.70, temperature 277K
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG3001reservoir
25 %(w/v)PEG80001reservoir
310 %glycerol1reservoir
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.99184
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2002 / Details: FLAT MIRROR
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99184 Å / Relative weight: 1
ReflectionResolution: 1.3→38.19 Å / Num. obs: 167310 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.67 Å2 / Rsym value: 0.076 / Net I/σ(I): 10.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.585 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 72 Å / Num. obs: 167354 / Num. measured all: 542582 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
REFMAC5.1.955refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→38.19 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.031 / SU ML: 0.036 / Isotropic thermal model: Isotropic/Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE MODEL OF THE ACTIVE SITE AROUND THE METAL (FE) IS APPARENTLY STILL INCOMPLETE, AND POSSIBLY A SUPERPOSITION OF STATES: THE METAL (FE) IS PARTIALLY OCCUPIED (REFINED IN SHELX). A LIGATING ...Details: THE MODEL OF THE ACTIVE SITE AROUND THE METAL (FE) IS APPARENTLY STILL INCOMPLETE, AND POSSIBLY A SUPERPOSITION OF STATES: THE METAL (FE) IS PARTIALLY OCCUPIED (REFINED IN SHELX). A LIGATING SIDE-CHAIN (H256) HAS DUAL CONFORMATION. OMIT DENSITY FOR THE NICOTINAMIDE RING IS WEAK. RESIDUAL DIFFERENCE DENSITY PEAKS PERSIST NEAR NICOTINAMIDE NC5 ATOM, NEAR ENOUGH TO COMPETE FOR METAL LIGATION. ONLY ONE STATE, THE MOST DEFENSIBLE ONE, HAS BEEN MODELLED. SHELX/CCP4/ TLS WERE ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.17 8371 5 %RANDOM
Rwork0.137 ---
obs0.139 158936 97.8 %-
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: 10.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-0.06 Å2
2--0.05 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5596 0 116 892 6604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225835
X-RAY DIFFRACTIONr_bond_other_d0.0020.025346
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9977919
X-RAY DIFFRACTIONr_angle_other_deg0.989312486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47524.222225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.553151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2521526
X-RAY DIFFRACTIONr_chiral_restr0.0930.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021101
X-RAY DIFFRACTIONr_nbd_refined0.2250.21249
X-RAY DIFFRACTIONr_nbd_other0.2350.26298
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.23323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2629
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.52423598
X-RAY DIFFRACTIONr_mcangle_it2.2935828
X-RAY DIFFRACTIONr_scbond_it4.11482237
X-RAY DIFFRACTIONr_scangle_it5.922112089
X-RAY DIFFRACTIONr_rigid_bond_restr1.571311181
X-RAY DIFFRACTIONr_sphericity_free6.2383894
X-RAY DIFFRACTIONr_sphericity_bonded2.969311057
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 627
Rwork0.268 11928
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)
10.9410.3670.11550.84770.11730.6968-0.02840.1393-0.1055-0.07160.0659-0.10710.06960.0559-0.03750.0045-0.00010.00080.0173-0.01830.019511.89143.34543.634
20.83620.32140.09510.86890.17820.79390.01670.13090.075-0.15570.01910.0106-0.11690.0202-0.03590.06610.00630.00310.0260.00120.017834.4251.73265.072
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 35913 - 371
21AE18001800
31AC900900
42BB-1 - 35811 - 370
52BF18011801
62BD900900
Refinement
*PLUS
Lowest resolution: 72 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.53

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