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- PDB-3rku: Substrate Fingerprint and the Structure of NADP+ Dependent Serine... -

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Basic information

Entry
Database: PDB / ID: 3rku
TitleSubstrate Fingerprint and the Structure of NADP+ Dependent Serine Dehydrogenase from Saccharomyces cerevisiae complexed with NADP+
ComponentsOxidoreductase YMR226C
KeywordsOXIDOREDUCTASE / substrate fingerprint / short chain oxidoreductase / Rossmann Fold
Function / homology
Function and homology information


3-hydroxy acid dehydrogenase / serine 3-dehydrogenase activity / acetoin metabolic process / diacetyl reductase ((S)-acetoin forming) (NAD+) activity / carbonyl reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleus / cytoplasm
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent 3-hydroxy acid dehydrogenase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsHuether, R. / Pacheco, C.M. / Duax, W.L.
CitationJournal: To be Published
Title: Substrate Fingerprint and the Structure of NADP+ Dependent Serine Dehydrogenase from Saccharomyces cerevisiae complexed with NADP+
Authors: Huether, R. / Pacheco, C.M. / Duax, W.L.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Oxidoreductase YMR226C
B: Oxidoreductase YMR226C
C: Oxidoreductase YMR226C
D: Oxidoreductase YMR226C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7938
Polymers125,8194
Non-polymers2,9744
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17410 Å2
ΔGint-76 kcal/mol
Surface area35850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.390, 87.250, 83.810
Angle α, β, γ (deg.)90.000, 112.980, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 0 - 267 / Label seq-ID: 20 - 287

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 0:267 )AA
2chain B and (resseq 0:267 )BB
3chain C and (resseq 0:267 )CC
4chain D and (resseq 0:267 )DD

NCS oper:
IDCodeMatrixVector
1given(0.413099, 0.033646, -0.910064), (0.035198, -0.99916, -0.020963), (-0.910005, -0.023372, -0.413937)23.514999, 85.694298, 39.754299
2given(-0.419343, -0.103043, 0.901961), (-0.105587, -0.981259, -0.161192), (0.901667, -0.16283, 0.400604)3.23659, 89.365402, 8.19826
3given(-0.997352, 0.071777, 0.011749), (0.072719, 0.980978, 0.179984), (0.001393, 0.180361, -0.983599)20.239201, -3.67247, 31.5373

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Components

#1: Protein
Oxidoreductase YMR226C / NADP+ Dependent Serine Dehydrogenase


Mass: 31454.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YM9959.08C, YMR226C / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q05016, Oxidoreductases
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% v/v MPD, 24% w/v PEG4000, 0.1 M ammonium thiocyanate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 8, 2010 / Details: Osmic VariMax Cu-HF optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.36→77.161 Å / Num. all: 45068 / Num. obs: 44993 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.06 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.135 / Χ2: 0.96 / Net I/σ(I): 6.3 / Scaling rejects: 916
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.36-2.443.660.48921186444491.1799.8
2.44-2.543.990.48521216244881.14100
2.54-2.6640.4512.21215444891.13100
2.66-2.84.020.3692.71212144931.1100
2.8-2.974.050.32831223744720.96100
2.97-3.24.060.2743.61222244850.9100
3.2-3.534.080.19551221744250.84100
3.53-4.034.080.1257.91234945090.81100
4.03-5.084.090.0999.41244445250.8299.9
5.08-45.874.040.0959.81230745930.7599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NWQ

2nwq


Resolution: 2.6→40.949 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.45 / σ(F): 1.33 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1668 4.94 %RANDOM
Rwork0.1885 ---
obs0.1913 33738 99.82 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.096 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 106.76 Å2 / Biso mean: 26.2043 Å2 / Biso min: 2.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.3431 Å20 Å21.3314 Å2
2--4.3966 Å20 Å2
3----1.0535 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8252 0 192 555 8999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118578
X-RAY DIFFRACTIONf_angle_d1.2811649
X-RAY DIFFRACTIONf_chiral_restr0.0781381
X-RAY DIFFRACTIONf_plane_restr0.0041485
X-RAY DIFFRACTIONf_dihedral_angle_d18.8373245
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2063X-RAY DIFFRACTIONPOSITIONAL0.054
12B2063X-RAY DIFFRACTIONPOSITIONAL0.054
13C2063X-RAY DIFFRACTIONPOSITIONAL0.059
14D2058X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.69290.41551510.2943322733783378100
2.6929-2.80070.32511770.2508316033373337100
2.8007-2.92820.31781500.2332320733573357100
2.9282-3.08250.27051820.2191317733593359100
3.0825-3.27550.27831700.2083318833583358100
3.2755-3.52830.26471750.2084320133763376100
3.5283-3.88310.26341450.1896321633613261100
3.8831-4.44450.2021610.1423321733783378100
4.4445-5.59730.17851970.1352319433913391100
5.5973-40.95360.17021600.157332833443344399
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)
10.31890.1936-0.03280.076-0.06220.23090.0709-0.02990.14180.0110.01110.0439-0.16150.1343-0.03770.01310.0445-0.0225-0.0169-0.00040.047333.7843.565426.547
20.6557-0.3978-0.17940.39830.17850.0550.06740.21380.0112-0.0326-0.0745-0.0394-0.052-0.01690.00570.07880.0230.00620.0730.02710.034114.776342.7477-2.9915
30.35450.1504-0.21410.0678-0.07180.0849-0.0353-0.0671-0.06830.01840.0560.03040.06760.0219-0.0120.05930.0075-0.01270.0168-0.00090.03498.572238.806642.282
40.4192-0.2177-0.25110.07580.23570.40360.06290.07450.0437-0.0026-0.0460.0027-0.049-0.0754-0.01280.02850.0178-0.00290.03160.00330.021-10.070146.452413.547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA0 - 267
2X-RAY DIFFRACTION2CHAIN BB0 - 267
3X-RAY DIFFRACTION3CHAIN CC0 - 267
4X-RAY DIFFRACTION4CHAIN DD0 - 267

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