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Basic information

Entry
Database: PDB / ID: 3uhj
TitleCrystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021
ComponentsProbable glycerol dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


glycerol dehydrogenase / glycerol dehydrogenase [NAD+] activity / metal ion binding
Similarity search - Function
Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold ...Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SELENIUM ATOM / Probable glycerol dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsAgarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a probable glycerol dehydrogenase from Sinorhizobium meliloti 1021
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_seq_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.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable glycerol dehydrogenase
B: Probable glycerol dehydrogenase
C: Probable glycerol dehydrogenase
D: Probable glycerol dehydrogenase
E: Probable glycerol dehydrogenase
F: Probable glycerol dehydrogenase
G: Probable glycerol dehydrogenase
H: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,77424
Polymers332,5408
Non-polymers1,23416
Water9,674537
1
A: Probable glycerol dehydrogenase
B: Probable glycerol dehydrogenase
C: Probable glycerol dehydrogenase
D: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,90012
Polymers166,2704
Non-polymers6308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Probable glycerol dehydrogenase
H: Probable glycerol dehydrogenase
hetero molecules

F: Probable glycerol dehydrogenase
G: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,87412
Polymers166,2704
Non-polymers6048
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_455x-1,y,z1
3
A: Probable glycerol dehydrogenase
B: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4506
Polymers83,1352
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-88 kcal/mol
Surface area24230 Å2
MethodPISA
4
C: Probable glycerol dehydrogenase
D: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4506
Polymers83,1352
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-84 kcal/mol
Surface area24340 Å2
MethodPISA
5
E: Probable glycerol dehydrogenase
H: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5167
Polymers83,1352
Non-polymers3815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-94 kcal/mol
Surface area24530 Å2
MethodPISA
6
F: Probable glycerol dehydrogenase
G: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3585
Polymers83,1352
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-82 kcal/mol
Surface area24320 Å2
MethodPISA
7
E: Probable glycerol dehydrogenase
H: Probable glycerol dehydrogenase
hetero molecules

F: Probable glycerol dehydrogenase
G: Probable glycerol dehydrogenase
hetero molecules

A: Probable glycerol dehydrogenase
B: Probable glycerol dehydrogenase
C: Probable glycerol dehydrogenase
D: Probable glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,77424
Polymers332,5408
Non-polymers1,23416
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area23410 Å2
ΔGint-404 kcal/mol
Surface area88280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.483, 98.996, 104.734
Angle α, β, γ (deg.)76.94, 83.38, 71.47
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Probable glycerol dehydrogenase


Mass: 41567.523 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: gldA, R02550, SMc02038 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q92MR2, glycerol dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SE / SELENIUM ATOM / Hydrogen selenide


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M NACL, 0.1M Bis-tris, 25% PEG 3350, 0.2M NDSB 221, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2011 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. all: 121795 / Num. obs: 121795 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.2
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11833 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQ3

1kq3


Resolution: 2.34→45.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.435 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.395 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26358 6116 5 %RANDOM
Rwork0.19654 ---
obs0.1999 115674 98.17 %-
all-121795 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.639 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.34→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20737 0 46 537 21320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02221092
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.96728667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94752822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13122.877810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29153243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.34115181
X-RAY DIFFRACTIONr_chiral_restr0.1270.23447
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115821
X-RAY DIFFRACTIONr_mcbond_it0.8121.514055
X-RAY DIFFRACTIONr_mcangle_it1.519222349
X-RAY DIFFRACTIONr_scbond_it2.98537037
X-RAY DIFFRACTIONr_scangle_it4.6974.56318
LS refinement shellResolution: 2.341→2.402 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 402 -
Rwork0.262 8092 -
obs--93.1 %

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