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- PDB-2x7h: Crystal structure of the human MGC45594 gene product in complex w... -

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Basic information

Entry
Database: PDB / ID: 2x7h
TitleCrystal structure of the human MGC45594 gene product in complex with fenoprofen
ComponentsZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


13,14-dehydro-15-oxoprostaglandin 13-reductase / 13-prostaglandin reductase activity / 15-oxoprostaglandin 13-oxidase 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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / 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 / FENOPROFEN / Prostaglandin reductase 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShafqat, N. / Yue, W.W. / Ugochukwu, E. / Niesen, F. / Vollmar, M. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Smee, C. / Arrowsmith, C. ...Shafqat, N. / Yue, W.W. / Ugochukwu, E. / Niesen, F. / Vollmar, M. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Smee, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Human Mgc45594 Gene Product in Complex with Fenoprofen
Authors: Shafqat, N. / Yue, W.W. / Ugochukwu, E. / Niesen, F. / Vollmar, M. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Smee, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
History
DepositionFeb 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,69823
Polymers78,9502
Non-polymers3,74721
Water7,440413
1
A: ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,74615
Polymers39,4751
Non-polymers2,27114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9518
Polymers39,4751
Non-polymers1,4767
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.600, 52.050, 75.730
Angle α, β, γ (deg.)94.28, 91.29, 102.18
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A22 - 267
2112B22 - 267
1212A281 - 362
2212B281 - 362

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Components

#1: Protein ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2 / MGC45594 GENE PRODUCT


Mass: 39475.199 Da / Num. of mol.: 2 / Fragment: DEHYDROGENASE REDUCTASE DOMAIN, RESIDUES 25-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2 / References: UniProt: Q8N4Q0, Oxidoreductases
#2: Chemical
ChemComp-PFN / FENOPROFEN / (2R)-2-(3-PHENOXYPHENYL)PROPANOIC ACID / Fenoprofen


Mass: 242.270 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H14O3 / Comment: antiinflammatory*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.47 Å3/Da / Density % sol: 50.21 % / Description: NONE
Crystal growDetails: 0.5M NA MALONATE PH7.0, 0.25W/V JEFFAMINE ED 2001_PH7.0, 8PH HEPES.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9809
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 1.6→31.52 Å / Num. obs: 84512 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WEK
Resolution: 1.6→75.46 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.971 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 1861 2.2 %RANDOM
Rwork0.16773 ---
obs0.16831 82638 92.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.748 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0.09 Å2-0.1 Å2
2--0.83 Å20.05 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→75.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5075 0 236 413 5724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225523
X-RAY DIFFRACTIONr_bond_other_d0.0020.023705
X-RAY DIFFRACTIONr_angle_refined_deg1.4582.0417495
X-RAY DIFFRACTIONr_angle_other_deg1.0393.0048950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87724.033181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34615866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.191522
X-RAY DIFFRACTIONr_chiral_restr0.080.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216042
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021010
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_it1.4433436
X-RAY DIFFRACTIONr_mcbond_other0.32131410
X-RAY DIFFRACTIONr_mcangle_it2.51155541
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.29582087
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.111111942
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
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1869tight positional0.060.05
2B1869tight positional0.060.05
1A2068medium positional0.060.5
2B2068medium positional0.060.5
1A1869tight thermal0.180.5
2B1869tight thermal0.180.5
1A2068medium thermal0.142
2B2068medium thermal0.142
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 138 -
Rwork0.294 5880 -
obs--88.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.62131.8811-0.16281.8274-0.14750.9635-0.15780.64530.4094-0.21270.19170.0665-0.137-0.0977-0.03390.1006-0.0492-0.01520.24930.08240.098-19.0089.474-13.466
22.57530.94940.28991.2074-0.18440.5388-0.05890.02650.3126-0.04030.00070.0036-0.16430.01230.05810.0807-0.04520.00360.14390.01020.0844-10.2759.344-2.692
30.61390.145-0.02370.6466-0.2830.76850.0101-0.016-0.06120.01280.0074-0.01340.0491-0.0156-0.01740.0161-0.03380.00370.1055-0.00040.0404-18.528-10.5248.992
43.2107-1.089-0.5922.72380.38550.66790.0297-0.04980.0441-0.07860.0095-0.44570.03780.2106-0.03920.0383-0.03340.01830.1858-0.00090.1139-0.664-5.5159.616
52.00940.37320.46011.2015-0.35241.6886-0.00690.2432-0.0848-0.24830.0313-0.0210.1662-0.0259-0.02440.0791-0.04110.0260.1641-0.03230.0412-13.492-7.655-10.042
61.6702-0.43931.17731.52-0.84046.46720.0273-0.296-0.24860.25930.09290.21670.5502-0.6039-0.12030.215-0.1190.0430.23870.04380.1703-5.454-23.53345.668
71.82710.36330.35521.1080.13794.18080.0627-0.1888-0.41990.1962-0.0347-0.05340.6880.2518-0.0280.17740.00570.00950.18630.05310.1396.209-21.53646.061
80.95190.269-0.45190.5217-0.14281.96250.022-0.08630.03820.0545-0.0214-0.02-0.10950.1082-0.00070.0258-0.03470.00660.11620.00110.053211.18-1.96734.315
90.87731.33440.58483.982.50456.43280.1271-0.26460.09950.6254-0.2036-0.0557-0.0680.3110.07660.182-0.0796-0.04480.41090.02450.106519.535-4.17549.997
102.05680.40630.0371.5714-0.34922.39790.0289-0.15980.10060.1809-0.0140.2317-0.0634-0.2487-0.01490.0753-0.00440.06330.18720.00180.0784-3.8-5.66746.028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 50
2X-RAY DIFFRACTION2A51 - 112
3X-RAY DIFFRACTION3A113 - 303
4X-RAY DIFFRACTION4A304 - 318
5X-RAY DIFFRACTION5A319 - 361
6X-RAY DIFFRACTION6B22 - 49
7X-RAY DIFFRACTION7B50 - 106
8X-RAY DIFFRACTION8B107 - 303
9X-RAY DIFFRACTION9B304 - 318
10X-RAY DIFFRACTION10B319 - 361

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