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Basic information

Entry
Database: PDB / ID: 2x1h
TitleCrystal structure of the human MGC45594 gene product in complex with raloxifene
ComponentsZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
KeywordsOXIDOREDUCTASE / PEROXISOME
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 / Chem-X1H / Prostaglandin reductase 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsShafqat, N. / Yue, W.W. / Pike, A.C.W. / Niesen, F. / Ugochukwu, E. / Krojer, T. / Chaikuad, A. / Smee, C. / Arrowsmith, C. / Weigelt, J. ...Shafqat, N. / Yue, W.W. / Pike, A.C.W. / Niesen, F. / Ugochukwu, E. / Krojer, T. / Chaikuad, A. / 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 Raloxifene
Authors: Shafqat, N. / Yue, W.W. / Pike, A.C.W. / Niesen, F. / Ugochukwu, E. / Krojer, T. / Chaikuad, A. / Smee, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
History
DepositionDec 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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)80,68612
Polymers77,4452
Non-polymers3,24110
Water10,485582
1
A: ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4057
Polymers38,7221
Non-polymers1,6826
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)40,2815
Polymers38,7221
Non-polymers1,5584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.650, 52.040, 75.440
Angle α, β, γ (deg.)94.32, 91.44, 102.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 283:361 )
211CHAIN B AND (RESSEQ 283:361 )
112CHAIN A AND (RESSEQ 22:272 )
212CHAIN B AND (RESSEQ 22:272 )

NCS ensembles :
ID
1
2

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Components

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


Mass: 38722.387 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-371
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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#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-X1H / [6-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOTHIOPHEN-3-YL](4-METHOXYPHENYL)METHANONE


Mass: 376.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H16O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.26 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: 1.6M NA MALONATE PH7.0, 1% W/V JEFFAMINE ED 2001, 0.1M HEPES PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 9, 2009
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→40.5 Å / Num. obs: 64609 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WEK

2wek


Resolution: 1.75→40.5 Å / SU ML: 0.26 / σ(F): 1.97 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 3282 5.1 %
Rwork0.2084 --
obs0.2102 64588 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.635 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6985 Å2-0.7626 Å2-0.3936 Å2
2--2.0445 Å20.0408 Å2
3----0.3459 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 217 582 5798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085375
X-RAY DIFFRACTIONf_angle_d1.7317329
X-RAY DIFFRACTIONf_dihedral_angle_d18.5121906
X-RAY DIFFRACTIONf_chiral_restr0.13845
X-RAY DIFFRACTIONf_plane_restr0.006918
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A598X-RAY DIFFRACTIONPOSITIONAL
12B598X-RAY DIFFRACTIONPOSITIONAL0.052
21A1817X-RAY DIFFRACTIONPOSITIONAL
22B1817X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77610.36711410.32322654X-RAY DIFFRACTION93
1.7761-1.80390.36561410.30382698X-RAY DIFFRACTION93
1.8039-1.83350.31071410.27642678X-RAY DIFFRACTION93
1.8335-1.86510.30571320.25372695X-RAY DIFFRACTION93
1.8651-1.8990.28761430.24252619X-RAY DIFFRACTION93
1.899-1.93550.26071530.23362733X-RAY DIFFRACTION93
1.9355-1.9750.29561500.22182610X-RAY DIFFRACTION93
1.975-2.0180.26811360.21842689X-RAY DIFFRACTION93
2.018-2.06490.26221220.22212665X-RAY DIFFRACTION93
2.0649-2.11650.26821350.20772719X-RAY DIFFRACTION94
2.1165-2.17380.24091520.21472661X-RAY DIFFRACTION93
2.1738-2.23770.25791460.19852659X-RAY DIFFRACTION93
2.2377-2.30990.22991420.19562681X-RAY DIFFRACTION93
2.3099-2.39250.26821560.19772640X-RAY DIFFRACTION93
2.3925-2.48830.25181250.20462735X-RAY DIFFRACTION93
2.4883-2.60150.22831450.20172679X-RAY DIFFRACTION93
2.6015-2.73860.23961550.2092638X-RAY DIFFRACTION92
2.7386-2.91020.25591350.20362666X-RAY DIFFRACTION93
2.9102-3.13480.21671480.20472643X-RAY DIFFRACTION93
3.1348-3.45010.23071520.19222590X-RAY DIFFRACTION90
3.4501-3.9490.18331340.17942532X-RAY DIFFRACTION88
3.949-4.97390.19071560.16552598X-RAY DIFFRACTION91
4.9739-40.5110.19571420.18542824X-RAY DIFFRACTION98
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)
10.1858-0.0554-0.00530.1415-0.1510.0892-0.02040.11790.0948-0.04070.01420.0217-0.10730.036-0.00010.0644-0.0222-0.01020.08250.02350.0722-10.89047.2564-5.5542
20.311-0.0331-0.09160.125-0.10590.0352-0.02310.0128-0.0252-0.0070.00630.0210.03920.007700.04640.0012-0.00430.0232-0.0090.0524-16.4619-18.39269.0949
30.01220.0423-0.00510.2398-0.06970.13570.00890.0988-0.02270.05380.00890.0555-0.0727-0.0572-0.00120.01540.00240.00930.02240.00110.0455-30.0013-11.848412.6929
40.1451-0.0596-0.1730.11080.02120.33720.0645-0.0904-0.00530.0348-0.01190.0828-0.11770.2180.02050.03120.0092-0.00220.0391-0.00490.0869-6.5185-3.96359.8806
50.20480.1378-0.05370.1026-0.02480.0503-0.00350.1893-0.1397-0.1530.0011-0.00610.1183-0.0818-0.03020.0962-0.00830.01710.1073-0.01290.0118-13.8278-8.6081-11.4532
60.6840.2373-0.49980.39450.14710.6924-0.0406-0.1441-0.22050.05190.0176-0.05240.2875-0.0278-0.16170.12360.0125-0.00790.0550.0370.0949-40.3846-15.75-28.4305
70.21270.1092-0.11130.30940.00720.370.0053-0.07740.11150.0564-0.00660.0132-0.16440.1341-0.00110.0849-0.01320.00150.0417-0.00690.0452-33.119310.237-41.4981
80.00550.06920.00670.09370.05280.01640.0579-0.1014-0.0159-0.0281-0.0493-0.04380.06260.02980.00020.06350.0074-0.00140.0493-0.00210.0477-34.00042.2067-54.7373
90.070.0065-0.09890.1086-0.04870.0901-0.0119-0.1746-0.1439-0.10720.0615-0.0372-0.11590.3547-0.04160.05780.0011-0.01370.14660.00760.0416-26.2862-2.6678-31.467
100.1110.0191-0.00750.1643-0.08820.20470.0445-0.17910.10430.0373-0.01040.1585-0.1033-0.30610.00090.07140.0190.04590.1414-0.00930.0978-49.3344-1.1832-30.0693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 22:141)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 142:242)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 243:293)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 294:321)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 322:362)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 22:141)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 142:242)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 243:293)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 294:321)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 322:362)

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