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- PDB-4mca: Crystal Structure of Glycerol Dehydrogenase from Serratia to 1.9A -

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Basic information

Entry
Database: PDB / ID: 4mca
TitleCrystal Structure of Glycerol Dehydrogenase from Serratia to 1.9A
ComponentsGlycerol dehydrogenase
KeywordsOXIDOREDUCTASE / Glycerol metabolism
Function / homologyDehydroquinate 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 / :
Function and homology information
Biological speciesSerratia plymuthica A30 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMusille, P.M. / Ortlund, E.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of glycerol dehydrogenase from Serratia
Authors: Musille, P.M. / Ortlund, E.A.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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

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Assembly

Deposited unit
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,28112
Polymers77,6052
Non-polymers67610
Water6,575365
1
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)626,25096
Polymers620,84216
Non-polymers5,40880
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area58910 Å2
ΔGint-1084 kcal/mol
Surface area190240 Å2
MethodPISA
2
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules

A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules

A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules

A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,12548
Polymers310,4218
Non-polymers2,70440
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area27400 Å2
ΔGint-535 kcal/mol
Surface area97170 Å2
MethodPISA
3
A: Glycerol dehydrogenase
hetero molecules

B: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,28112
Polymers77,6052
Non-polymers67610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
Buried area4420 Å2
ΔGint-120 kcal/mol
Surface area26720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.507, 117.507, 259.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Glycerol dehydrogenase /


Mass: 38802.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Serratia plymuthica A30 (bacteria) / References: UniProt: L0VUH7, glycerol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 5-10% PEG 3350, 0.2M Calcium Acetate, 4% 2,2,2 trifluoroethanol, 4% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 71425 / Num. obs: 65891 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.46 / Num. unique all: 3706 / % possible all: 52.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.5.3phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2009 / WRfactor Rwork: 0.1647 / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8584 / SU B: 3.037 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1353 / SU Rfree: 0.1304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 3341 5.1 %RANDOM
Rwork0.1771 ---
obs0.179 65855 91.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.78 Å2 / Biso mean: 30.0239 Å2 / Biso min: 11.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20 Å2
2--1.65 Å20 Å2
3----3.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5397 0 30 365 5792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195515
X-RAY DIFFRACTIONr_bond_other_d0.0010.025395
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9617478
X-RAY DIFFRACTIONr_angle_other_deg0.913312380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1195729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73424.593209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88615896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0391520
X-RAY DIFFRACTIONr_chiral_restr0.1250.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021200
X-RAY DIFFRACTIONr_mcbond_it2.652.672919
X-RAY DIFFRACTIONr_mcbond_other2.6432.6692918
X-RAY DIFFRACTIONr_mcangle_it3.6883.9853644
LS refinement shellResolution: 1.898→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 110 -
Rwork0.258 2473 -
all-2583 -
obs--49.33 %

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