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- PDB-3ce9: Crystal structure of glycerol dehydrogenase (NP_348253.1) from Cl... -

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Basic information

Entry
Database: PDB / ID: 3ce9
TitleCrystal structure of glycerol dehydrogenase (NP_348253.1) from Clostridium acetobutylicum at 2.37 A resolution
ComponentsGlycerol dehydrogenase
KeywordsOXIDOREDUCTASE / NP_348253.1 / glycerol dehydrogenase / 3-dehydroquinate synthase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / phospholipid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Glycerol-1-phosphate dehydrogenase / Iron-containing alcohol dehydrogenase / Glycerol 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
DI(HYDROXYETHYL)ETHER / Glycerol dehydrogenase
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.37 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of glycerol dehydrogenase (NP_348253.1) from Clostridium acetobutylicum at 2.37 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 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
Revision 1.5Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)159,67525
Polymers158,2704
Non-polymers1,40521
Water3,585199
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-58.9 kcal/mol
Surface area51310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.740, 125.810, 133.230
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILEAA5 - 216 - 22
21SERSERILEILEBB5 - 216 - 22
31SERSERILEILECC5 - 216 - 22
41SERSERILEILEDD5 - 216 - 22
52ASNASNVALVALAA23 - 35324 - 354
62ASNASNLEULEUBB23 - 35224 - 353
72ASNASNVALVALCC23 - 35324 - 354
82ASNASNVALVALDD23 - 35324 - 354
DetailsACCORDING TO AUTHORS, THE CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE PROTEIN IS TETRAMERIC.

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Components

#1: Protein
Glycerol dehydrogenase


Mass: 39567.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Species: Clostridium acetobutylicum / Strain: DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 / Gene: NP_348253.1, CA_C1626 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97IL4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 0.2M NaCl, 20.0% PEG 3000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97953, 0.97939
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979531
30.979391
ReflectionResolution: 2.37→28.94 Å / Num. obs: 66387 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.802 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.37-2.450.4011.81273811600191.4
2.45-2.550.3142.31536313429198.5
2.55-2.670.2313.11569313573198.5
2.67-2.810.1823.91515413033198.2
2.81-2.980.1295.41482312641198.1
2.98-3.210.0897.31543613106197.7
3.21-3.540.0610.11586613349197.5
3.54-4.040.04712.41531012711197.5
4.04-5.080.03317.11576912972196.7
5.08-28.940.0318.51560512777194.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.37→28.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 13.863 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.217
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ZINC IONS HAVE BEEN MODELED INTO THE PUTATIVE ACTIVE SITE BASED ON FLUORESCENCE SCAN, ANOMALOUS ELECTRON DENSITY MAPS AND COORDINATION GEOMETRY. 5. 1,2-ETHANEDIOL AND PEG MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3364 5.1 %RANDOM
Rwork0.188 ---
obs0.189 66387 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.094 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.55 Å2
2---0.79 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.37→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10663 0 78 199 10940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211028
X-RAY DIFFRACTIONr_bond_other_d0.0020.027368
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9614916
X-RAY DIFFRACTIONr_angle_other_deg1.256318138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.24951419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02625.056445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.189151912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4421534
X-RAY DIFFRACTIONr_chiral_restr0.0690.21735
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212230
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022112
X-RAY DIFFRACTIONr_mcbond_it0.98736988
X-RAY DIFFRACTIONr_mcbond_other0.23632855
X-RAY DIFFRACTIONr_mcangle_it1.979411349
X-RAY DIFFRACTIONr_scbond_it3.71964040
X-RAY DIFFRACTIONr_scangle_it5.81793560
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2027TIGHT POSITIONAL0.040.05
2B2027TIGHT POSITIONAL0.040.05
3C2027TIGHT POSITIONAL0.030.05
4D2027TIGHT POSITIONAL0.040.05
1A2172MEDIUM POSITIONAL0.050.5
2B2172MEDIUM POSITIONAL0.050.5
3C2172MEDIUM POSITIONAL0.040.5
4D2172MEDIUM POSITIONAL0.050.5
1A2027TIGHT THERMAL0.10.5
2B2027TIGHT THERMAL0.10.5
3C2027TIGHT THERMAL0.10.5
4D2027TIGHT THERMAL0.110.5
1A2172MEDIUM THERMAL0.092
2B2172MEDIUM THERMAL0.12
3C2172MEDIUM THERMAL0.092
4D2172MEDIUM THERMAL0.122
LS refinement shellResolution: 2.37→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 231 -
Rwork0.3 4520 -
all-4751 -
obs--95.57 %
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)
11.1975-0.1074-0.30151.203-0.12511.1435-0.0827-0.0237-0.04480.30880.04430.00560.0821-0.08140.03830.0073-0.0121-0.1003-0.08160.0049-0.120431.92826.911-2.093
22.57560.13410.12150.9949-0.09720.7320.04630.0418-0.42310.07880.0109-0.17690.07230.1502-0.0572-0.0754-0.0241-0.0699-0.0684-0.04460.072520.7462.736-24.819
31.6228-0.3193-0.38711.37890.08051.40680.02770.0974-0.0335-0.2181-0.02150.1655-0.0819-0.0422-0.0062-0.0383-0.0362-0.0764-0.09730.008-0.08716.3930.455-47.037
41.6290.4979-0.07911.3236-0.14460.9623-0.038-0.00460.17560.03340.01840.0715-0.0741-0.12990.0196-0.1072-0.0006-0.0542-0.1154-0.0256-0.038521.35454.529-25.952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 3536 - 354
2X-RAY DIFFRACTION2BB5 - 3526 - 353
3X-RAY DIFFRACTION3CC5 - 3536 - 354
4X-RAY DIFFRACTION4DD5 - 3536 - 354

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