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- PDB-1xg5: Structure of human putative dehydrogenase MGC4172 in complex with NADP -

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Basic information

Entry
Database: PDB / ID: 1xg5
TitleStructure of human putative dehydrogenase MGC4172 in complex with NADP
ComponentsARPG836
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase / Human / SGC / structural genomics / Structural Genomics Consortium
Function / homology
Function and homology information


3beta-hydroxysteroid 3-dehydrogenase / 3-keto sterol reductase activity / 17-beta-ketosteroid reductase activity / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / steroid biosynthetic process / nucleotide binding / extracellular region
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dehydrogenase/reductase SDR family member 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsKavanagh, K. / Ng, S. / Sharma, S. / Vedadi, M. / von Delft, F. / Walker, J.R. / dhe Paganon, S. / Bray, J. / Oppermann, U. / Edwards, A. ...Kavanagh, K. / Ng, S. / Sharma, S. / Vedadi, M. / von Delft, F. / Walker, J.R. / dhe Paganon, S. / Bray, J. / Oppermann, U. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structural Genomics Consortium: Structure of the putative human dehydrogenase MGC4172
Authors: Kavanagh, K. / Ng, S. / Sharma, S. / Vedadi, M. / von Delft, F. / Walker, J.R. / dhe Paganon, S. / Bray, J. / Oppermann, U. / Edwards, A. / Arrowsmith, C. / Sundstrom, M.
History
DepositionSep 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 25, 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_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_ref_seq_dif.details / _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: ARPG836
B: ARPG836
C: ARPG836
D: ARPG836
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,02011
Polymers121,8664
Non-polymers3,1547
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-80 kcal/mol
Surface area34260 Å2
MethodPISA
2
A: ARPG836
D: ARPG836
hetero molecules

B: ARPG836
C: ARPG836
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,02011
Polymers121,8664
Non-polymers3,1547
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area13470 Å2
ΔGint-69 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.710, 124.669, 75.130
Angle α, β, γ (deg.)90.00, 97.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer, contained in one asymmetric unit.

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Components

#1: Protein
ARPG836 / MGC4172 gene product


Mass: 30466.518 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGC4172 / Plasmid: p11 (pET11 derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta2 / References: UniProt: Q6UWP2
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 859 / 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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM Bis-Tris pH 5.5, 200mM Ammonium Acetate, 2% Glycerol (total 7%), 18% PEG 3350, 0.5mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2004
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→41.56 Å / Num. all: 149996 / Num. obs: 145577 / % possible obs: 97.05 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 14.99 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 13
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.6 / Num. unique all: 8970 / Rsym value: 0.558 / % possible all: 81.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EDO

1edo


Resolution: 1.53→41.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.004 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual isotropic thermal parameters
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2) PROMINENT DIFFERENCE DENSITY AROUND RESIDUES A208, C208, D208 AND B151 WAS NOT INTERPRETABLE AND WAS LEFT UNMODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20638 1920 1.3 %RANDOM
Rwork0.1617 ---
all0.16226 145565 --
obs0.16226 143645 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.172 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20.27 Å2
2---0.86 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.53→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7549 0 204 859 8612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0218057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.98910999
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56851041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82423.636319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.995151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1351560
X-RAY DIFFRACTIONr_chiral_restr0.1060.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.24020
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25624
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2780
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9411.55246
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44828220
X-RAY DIFFRACTIONr_scbond_it2.41133153
X-RAY DIFFRACTIONr_scangle_it3.6174.52764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 131 -
Rwork0.26 8836 -
obs--81.13 %
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)
10.546-0.03830.0051.81410.83771.52670.0158-0.1238-0.06210.4484-0.0204-0.09450.20170.05760.0047-0.0145-0.0095-0.0136-0.11610.0223-0.129510.01157.36722.3596
20.9454-0.20840.60690.9133-0.24461.28670.0258-0.13880.03950.1983-0.0387-0.0527-0.125-0.05550.0129-0.1046-0.0045-0.0173-0.108-0.0089-0.09920.358286.277915.2491
30.78930.22290.17211.19360.08171.6066-0.03320.0745-0.0422-0.17230.0156-0.0497-0.0460.05410.0176-0.13620.00590.0265-0.1374-0.0001-0.143712.64280.5806-16.819
40.88190.2994-0.09051.1943-0.04131.27380.04270.0697-0.001-0.0972-0.02750.0789-0.0036-0.1201-0.0151-0.16770.00530.0037-0.13570.0004-0.1219-0.453653.0569-8.7285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 258
2X-RAY DIFFRACTION2B2 - 258
3X-RAY DIFFRACTION3C2 - 258
4X-RAY DIFFRACTION4D2 - 258

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