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- PDB-2c0c: Structure of the MGC45594 gene product -

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Basic information

Entry
Database: PDB / ID: 2c0c
TitleStructure of the MGC45594 gene product
ComponentsZINC BINDING ALCOHOL DEHYDROGENASE, DOMAIN CONTAINING 2
KeywordsOXIDOREDUCTASE / QUINONE OXIDOREDUCTASE / MEDIUM-CHAIN DEHYDROGENASE/REDUCTASE
Function / homology
Function and homology information


13,14-dehydro-15-oxoprostaglandin 13-reductase / : / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / negative regulation of fat cell differentiation / peroxisome / zinc ion binding
Similarity search - Function
: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal ...: / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Prostaglandin reductase 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBunkoczi, G. / Shafqat, N. / Guo, K. / Smee, C. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Gileadi, O. / von Delft, F. / Oppermann, U.
CitationJournal: To be Published
Title: The Structure of Mgc45594 Gene Product
Authors: Bunkoczi, G. / Shafqat, N. / Guo, K. / Smee, C. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Gileadi, O. / von Delft, F. / Oppermann, U.
History
DepositionAug 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZINC BINDING ALCOHOL DEHYDROGENASE, DOMAIN CONTAINING 2
B: ZINC BINDING ALCOHOL DEHYDROGENASE, DOMAIN CONTAINING 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9324
Polymers77,4452
Non-polymers1,4872
Water12,142674
1
A: ZINC BINDING ALCOHOL DEHYDROGENASE, DOMAIN CONTAINING 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4662
Polymers38,7221
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ZINC BINDING ALCOHOL DEHYDROGENASE, DOMAIN CONTAINING 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4662
Polymers38,7221
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.164, 82.137, 73.905
Angle α, β, γ (deg.)90.00, 112.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9675, 0.20263, 0.15125), (0.22852, 0.4447, 0.86604), (0.10823, 0.87246, -0.47655)
Vector: 73.81544, 19.17183, -49.96343)

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Components

#1: Protein ZINC BINDING ALCOHOL DEHYDROGENASE, DOMAIN CONTAINING 2 / MGC45594 HYPOTHETICAL PROTEIN


Mass: 38722.387 Da / Num. of mol.: 2 / Fragment: DOMAIN, RESIDUES 33-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N4Q0
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 9.1 / Details: 0.1 M BICINE PH=9.1 24% PEG 10K, pH 9.10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 5, 2005
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.45→46.5 Å / Num. obs: 116573 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.89 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.24
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 3.18 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.27 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QOR

1qor


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.179 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5848 5 %RANDOM
Rwork0.163 ---
obs0.166 110704 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-1.03 Å2
2---0.54 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 96 674 5933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225470
X-RAY DIFFRACTIONr_bond_other_d0.0010.025052
X-RAY DIFFRACTIONr_angle_refined_deg1.7642.0137466
X-RAY DIFFRACTIONr_angle_other_deg0.903311777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98224190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83515890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9351524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.210.21039
X-RAY DIFFRACTIONr_nbd_other0.1850.25046
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22727
X-RAY DIFFRACTIONr_nbtor_other0.0890.23328
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.2206
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.2148
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.60533658
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.49155640
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.61882155
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.07111813
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 434
Rwork0.282 8020

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