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- PDB-5xn8: Structure of glycerol dehydrogenase crystallised as a contaminant -

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Basic information

Entry
Database: PDB / ID: 5xn8
TitleStructure of glycerol dehydrogenase crystallised as a contaminant
ComponentsGlycerol Dehydrogenase
KeywordsOXIDOREDUCTASE / MarathonMR / Glycerol dehydrogenase / contamination
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 speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsHatti, K. / Mathiharan, Y.K. / Srinivasan, N. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2017
Title: Seeing but not believing: the structure of glycerol dehydrogenase initially assumed to be the structure of a survival protein from Salmonella typhimurium
Authors: Hatti, K. / Mathiharan, Y.K. / Srinivasan, N. / Murthy, M.R.N.
History
DepositionMay 19, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 7, 2017ID: 5WQ5
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 16, 2017Group: Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.3Sep 5, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Nov 22, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)156,34010
Polymers155,8944
Non-polymers4466
Water2,738152
1
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)312,68120
Polymers311,7898
Non-polymers89212
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_375-x-2,-y+2,z1
crystal symmetry operation3_575-y,x+2,z1
crystal symmetry operation4_355y-2,-x,z1
Buried area23400 Å2
ΔGint-411 kcal/mol
Surface area97720 Å2
MethodPISA
2
C: Glycerol Dehydrogenase
D: Glycerol Dehydrogenase
hetero molecules

C: Glycerol Dehydrogenase
D: Glycerol Dehydrogenase
hetero molecules

C: Glycerol Dehydrogenase
D: Glycerol Dehydrogenase
hetero molecules

C: Glycerol Dehydrogenase
D: Glycerol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,68120
Polymers311,7898
Non-polymers89212
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area23490 Å2
ΔGint-419 kcal/mol
Surface area97330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.550, 178.550, 80.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 365 / Label seq-ID: 1 - 365

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Glycerol Dehydrogenase


Mass: 38973.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: 0.1 M HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), pH 7.5, 0.02 M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.176
11-H, K, -L20.824
ReflectionResolution: 2.33→56.46 Å / Num. obs: 96487 / % possible obs: 89.3 % / Redundancy: 6.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.07
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.37 / Num. unique obs: 4048 / CC1/2: 0.64 / % possible all: 51.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MCA

4mca


Resolution: 2.33→56.46 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.865 / SU B: 10.824 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.046 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25146 4831 5 %RANDOM
Rwork0.23598 ---
obs0.23676 91655 89.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 33.661 Å2
Baniso -1Baniso -2Baniso -3
1-9.29 Å20 Å20 Å2
2--9.29 Å20 Å2
3----18.57 Å2
Refinement stepCycle: 1 / Resolution: 2.33→56.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 16 152 11100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911181
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210584
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.96415171
X-RAY DIFFRACTIONr_angle_other_deg0.912324519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54151463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94624.726438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.351151854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.691541
X-RAY DIFFRACTIONr_chiral_restr0.0680.21779
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022144
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.7655855
X-RAY DIFFRACTIONr_mcbond_other0.941.7655854
X-RAY DIFFRACTIONr_mcangle_it1.5222.6477317
X-RAY DIFFRACTIONr_mcangle_other1.5222.6477318
X-RAY DIFFRACTIONr_scbond_it0.8771.8395326
X-RAY DIFFRACTIONr_scbond_other0.8751.8395326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3952.7237855
X-RAY DIFFRACTIONr_long_range_B_refined2.67721.13512196
X-RAY DIFFRACTIONr_long_range_B_other2.6621.12912183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A225320.07
12B225320.07
21A227640.07
22C227640.07
31A226180.08
32D226180.08
41B224740.07
42C224740.07
51B225140.07
52D225140.07
61C224400.07
62D224400.07
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 208 -
Rwork0.309 4048 -
obs--53.56 %
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)
10.83270.03950.11840.19820.0110.47710.0350.0435-0.0667-0.03160.0013-0.07050.14640.086-0.03630.22440.0451-0.00330.1524-0.02480.032-154.949151.7412.957
20.32470.0589-0.12630.67390.28080.70970.0203-0.0878-0.06070.0894-0.0058-0.15610.10610.1687-0.01450.19610.0419-0.02730.22140.00090.0473-148.342159.43235.177
30.5943-0.12450.02560.6399-0.11450.66110.0041-0.04790.09560.05840.00590.0071-0.1088-0.0711-0.00990.21110.05620.01620.1869-0.01860.0199-108.036119.727-1.269
40.8806-0.283-0.10970.43040.24230.7320.03260.0740.1824-0.0768-0.00430.0201-0.2107-0.0624-0.02820.2760.0390.01280.19460.03340.0614-98.762123.784-33.548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 365
2X-RAY DIFFRACTION2B1 - 365
3X-RAY DIFFRACTION3C1 - 365
4X-RAY DIFFRACTION4D1 - 365

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