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- PDB-1kq3: CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERM... -

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Basic information

Entry
Database: PDB / ID: 1kq3
TitleCRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION
Componentsglycerol dehydrogenase
KeywordsOXIDOREDUCTASE / GLYCEROL DEHYDROGENASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


anaerobic glycerol catabolic process / glycerol dehydrogenase (NAD+) activity / glycerol dehydrogenase / metal ion binding / cytosol
Similarity search - Function
Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / 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 ...Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / 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
Glycerol dehydrogenase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsWilson, I.A. / Miller, M.D. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
Authors: Lesley, S.A. / Kuhn, P. / Godzik, A. / Deacon, A.M. / Mathews, I. / Kreusch, A. / Spraggon, G. / Klock, H.E. / McMullan, D. / Shin, T. / Vincent, J. / Robb, A. / Brinen, L.S. / Miller, M.D. ...Authors: Lesley, S.A. / Kuhn, P. / Godzik, A. / Deacon, A.M. / Mathews, I. / Kreusch, A. / Spraggon, G. / Klock, H.E. / McMullan, D. / Shin, T. / Vincent, J. / Robb, A. / Brinen, L.S. / Miller, M.D. / McPhillips, T.M. / Miller, M.A. / Scheibe, D. / Canaves, J.M. / Guda, C. / Jaroszewski, L. / Selby, T.L. / Elsliger, M.-A. / Wooley, J. / Taylor, S.S. / Hodgson, K.O. / Wilson, I.A. / Schultz, P.G. / Stevens, R.C.
History
DepositionJan 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 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_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_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.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_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_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_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: glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4214
Polymers41,1981
Non-polymers2233
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: glycerol dehydrogenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)331,36932
Polymers329,5858
Non-polymers1,78424
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area32390 Å2
ΔGint-526 kcal/mol
Surface area94950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.730, 105.730, 135.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-2995-

HOH

DetailsThe functional molecule is a monomer. The coordinates describe the asymmetric unit.

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Components

#1: Protein glycerol dehydrogenase /


Mass: 41198.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0423 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WYQ4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / pH: 6.2
Details: 35% MPD, 0.1M Na/k phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.20
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 29, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 61417 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.044 / Net I/σ(I): 9.1
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.234 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2
Reflection shell
*PLUS
Redundancy: 4.5 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / σ(F): 2
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3082 5 %RANDOM
Rwork0.173 ---
obs0.173 61064 --
all-61525 --
Displacement parametersBiso mean: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.396 Å20 Å20 Å2
2--0.396 Å20 Å2
3----0.793 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 10 227 3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.0241.5
X-RAY DIFFRACTIONc_mcangle_it1.5182
X-RAY DIFFRACTIONc_scbond_it2.1582
X-RAY DIFFRACTIONc_scangle_it3.132.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4TRIS.PARAM
X-RAY DIFFRACTION5
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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