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- PDB-4b4o: Crystal Structure of human epimerase family protein SDR39U1 (isof... -

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Basic information

Entry
Database: PDB / ID: 4b4o
TitleCrystal Structure of human epimerase family protein SDR39U1 (isoform2) with NADPH
ComponentsEPIMERASE FAMILY PROTEIN SDR39U1
KeywordsISOMERASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / mitochondrion / nucleus
Similarity search - Function
Epimerase family protein SDR39U1 / Domain of unknown function DUF1731 / Domain of unknown function (DUF1731) / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Epimerase family protein SDR39U1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsVollmar, M. / Muniz, J.R.C. / Shafqat, N. / Picaud, S. / Krojer, T. / Chaikuad, A. / Pike, A.C.W. / Yue, W.W. / Filippakopoulos, P. / Kavanagh, K.L. ...Vollmar, M. / Muniz, J.R.C. / Shafqat, N. / Picaud, S. / Krojer, T. / Chaikuad, A. / Pike, A.C.W. / Yue, W.W. / Filippakopoulos, P. / Kavanagh, K.L. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Epimerase Family Protein Sdr39U1 (Isoform2) with Nadph
Authors: Vollmar, M. / Muniz, J.R.C. / Shafqat, N. / Picaud, S. / Krojer, T. / Chaikuad, A. / Pike, A.C.W. / Yue, W.W. / Filippakopoulos, P. / Kavanagh, K.L. / von Delft, F. / Weigelt, J. / ...Authors: Vollmar, M. / Muniz, J.R.C. / Shafqat, N. / Picaud, S. / Krojer, T. / Chaikuad, A. / Pike, A.C.W. / Yue, W.W. / Filippakopoulos, P. / Kavanagh, K.L. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
History
DepositionJul 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: EPIMERASE FAMILY PROTEIN SDR39U1
B: EPIMERASE FAMILY PROTEIN SDR39U1
C: EPIMERASE FAMILY PROTEIN SDR39U1
D: EPIMERASE FAMILY PROTEIN SDR39U1
E: EPIMERASE FAMILY PROTEIN SDR39U1
F: EPIMERASE FAMILY PROTEIN SDR39U1
G: EPIMERASE FAMILY PROTEIN SDR39U1
H: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,23924
Polymers256,4408
Non-polymers8,79916
Water9,368520
1
A: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1553
Polymers32,0551
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1553
Polymers32,0551
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1553
Polymers32,0551
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1553
Polymers32,0551
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1553
Polymers32,0551
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1553
Polymers32,0551
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1553
Polymers32,0551
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: EPIMERASE FAMILY PROTEIN SDR39U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1553
Polymers32,0551
Non-polymers1,1002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.824, 83.362, 105.191
Angle α, β, γ (deg.)89.93, 76.73, 71.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
EPIMERASE FAMILY PROTEIN SDR39U1 / SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY 39U MEMBER 1


Mass: 32054.963 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ISOFORM2 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q9NRG7
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPOLYETHYLENE GLYCOL (PE4): FRAGMENT OF SUSPECTED PEG3350 FROM CRYSTALLISATION
Sequence detailsC TERMINAL RESIDUES AENL ARE DUE TO CLONING

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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: 2.42 Å3/Da / Density % sol: 49.2 % / Description: NONE
Crystal growDetails: 0.2M NA FORMATE 15W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 68174 / % possible obs: 98.2 % / Observed criterion σ(I): 4.1 / Redundancy: 7.9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 4.1 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→102.07 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / SU B: 19.214 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23074 3466 5.1 %RANDOM
Rwork0.19791 ---
obs0.19958 64704 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.159 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.42 Å2-0.04 Å2
2--0.05 Å2-0.2 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.7→102.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17382 0 536 520 18438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01918400
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212165
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.99725117
X-RAY DIFFRACTIONr_angle_other_deg1.4193.00529629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80552363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27123.218696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.772152508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.59115118
X-RAY DIFFRACTIONr_chiral_restr0.0690.22830
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120573
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023801
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 226 -
Rwork0.317 4362 -
obs--89.07 %
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)
12.3992-0.03141.30772.47040.09462.42230.20460.1525-0.2969-0.3259-0.12320.27460.3376-0.1252-0.08140.20330.0494-0.03550.1348-0.06240.220844.9404-58.2004-46.5109
21.4322-0.708-0.97771.43981.28072.67760.05490.1137-0.0319-0.0153-0.07280.0843-0.0022-0.05930.01790.1148-0.0038-0.02620.09190.00980.157747.6742-45.3277-33.9814
33.51030.7752-2.47282.0891-1.12583.39520.0119-0.08280.05050.0080.03250.1142-0.0724-0.0899-0.04440.1032-0.0272-0.08420.1138-0.04580.13648.2814-46.3288-29.8684
41.5567-0.18630.64722.3673-0.67672.49480.0607-0.1572-0.27490.0489-0.01920.01550.3692-0.1097-0.04150.1621-0.01140.03510.13870.00230.194772.6319-84.9331-41.7964
51.70550.1749-2.15720.6579-0.23953.222-0.073-0.0394-0.1145-0.0163-0.0177-0.0573-0.04550.06580.09070.15520.0387-0.01140.0859-0.00520.137477.6669-72.9376-53.5505
61.5333-1.2167-1.81453.11912.79474.19420.19950.15370.1081-0.0742-0.053-0.183-0.070.0207-0.14650.17540.0431-0.05080.13660.08250.128777.3152-73.2879-58.5102
71.58930.3293-0.04581.8689-0.34583.27510.0725-0.06010.08520.2795-0.0129-0.0882-0.26210.2171-0.05960.14450.0377-0.01660.15310.00840.180357.3694-15.5243-50.7302
81.7671-0.61621.17631.2558-0.48661.4193-0.01050.00990.0010.0018-0.02760.07260.10490.0040.03810.18290.06110.03830.14170.00060.153248.7127-17.7934-65.6779
93.1557-1.92050.54466.85010.87182.18360.07350.2121-0.0048-0.0384-0.10050.17710.02810.05320.0270.15680.02360.03750.20230.00550.014548.3337-14.7318-68.8695
101.26180.8726-0.28684.3468-0.52840.4045-0.01040.1519-0.1885-0.3590.1062-0.25370.18740.0757-0.09580.1665-0.0016-0.01710.2099-0.06250.168290.0385-51.3567-43.8964
112.1514-0.12151.42751.4434-0.10042.1573-0.01030.01390.11440.0138-0.0201-0.0385-0.2-0.03050.03040.1399-0.01960.04630.1637-0.01150.154490.2247-43.6368-28.0299
125.35192.47990.73753.4541-0.67651.13920.0363-0.372-0.155-0.050.0531-0.18020.1048-0.0761-0.08940.1909-0.0170.05070.24970.00070.06896.0954-47.8404-19.3115
131.45140.0587-0.47612.3849-0.2643.9401-0.08360.26270.3392-0.427-0.02170.0832-0.3764-0.02240.10520.29010.0376-0.05790.16740.02310.294176.553-36.5972-86.9549
142.708-1.15311.51411.9379-0.80821.3135-0.03190.1210.135-0.1744-0.00650.00070.0739-0.09320.03850.1751-0.01640.0030.1525-0.00690.14378.5007-50.9331-77.3164
155.77921.30152.36792.28951.29252.1528-0.0356-0.1801-0.1565-0.19720.07460.013-0.06390.0382-0.0390.18540.00140.08340.15110.07820.100880.7151-51.106-72.7876
161.65880.28830.00352.8242-1.02642.40430.0207-0.0297-0.2050.05330.0411-0.13170.2070.2113-0.06170.15890.0638-0.01480.1929-0.03260.18668.4575-79.2148-90.6218
170.98130.0755-0.39951.10030.53463.2201-0.041-0.0351-0.00730.02690.01690.0197-0.0079-0.17460.02410.16620.0446-0.0150.14310.00850.157758.7151-75.5971-102.2186
181.3542-1.9343-0.80536.8341.25932.46250.07440.20540.0013-0.08370.006-0.1869-0.1932-0.0526-0.08050.17130.0255-0.07210.20580.01960.127461.7814-76.4811-112.0925
191.263-0.41350.69512.121-0.18742.703-0.00020.1034-0.084-0.15170.11150.14020.1402-0.0551-0.11130.1129-0.01870.0160.175-0.00320.15632.667-51.583-97.3964
202.2020.1436-1.42741.3055-0.09572.2406-0.11990.01420.06950.13240.089-0.01430.07010.07080.03090.11310.0113-0.01810.1480.00180.132333.7856-47.2522-79.0258
214.58962.3169-1.28253.1399-0.16361.5547-0.1117-0.12860.0670.09530.18730.0897-0.00690.0249-0.07560.13080.0576-0.08520.18710.03650.109633.7221-50.5088-78.0322
221.95040.82320.4161.78390.36323.056-0.007-0.16350.19570.1227-0.0941-0.0284-0.42870.23120.10110.2626-0.09630.01220.2350.00170.20644.8762-10.053-103.7267
231.30670.26910.2010.82560.19391.6317-0.00520.08540.0103-0.00770.0033-0.07720.03220.2250.0020.2183-0.03730.0210.1406-0.00910.129134.5266-20.6563-114.3687
243.4781-2.45841.68274.4349-1.69462.22650.11140.1449-0.14230.0022-0.13850.1632-0.07520.12950.02710.216-0.05940.04460.1851-0.06850.06533.753-18.3892-117.2164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 150
2X-RAY DIFFRACTION2A151 - 238
3X-RAY DIFFRACTION3A239 - 295
4X-RAY DIFFRACTION4B1 - 149
5X-RAY DIFFRACTION5B150 - 237
6X-RAY DIFFRACTION6B238 - 295
7X-RAY DIFFRACTION7C1 - 149
8X-RAY DIFFRACTION8C150 - 237
9X-RAY DIFFRACTION9C238 - 295
10X-RAY DIFFRACTION10D1 - 63
11X-RAY DIFFRACTION11D66 - 237
12X-RAY DIFFRACTION12D238 - 295
13X-RAY DIFFRACTION13E1 - 149
14X-RAY DIFFRACTION14E150 - 237
15X-RAY DIFFRACTION15E238 - 295
16X-RAY DIFFRACTION16F1 - 87
17X-RAY DIFFRACTION17F88 - 237
18X-RAY DIFFRACTION18F238 - 295
19X-RAY DIFFRACTION19G1 - 168
20X-RAY DIFFRACTION20G169 - 237
21X-RAY DIFFRACTION21G238 - 295
22X-RAY DIFFRACTION22H1 - 171
23X-RAY DIFFRACTION23H172 - 237
24X-RAY DIFFRACTION24H238 - 295

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