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- PDB-1vkh: CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM S... -

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Basic information

Entry
Database: PDB / ID: 1vkh
TitleCRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION
Componentsputative serine hydrolase
KeywordsHYDROLASE / PUTATIVE SERINE HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


arylformamidase / arylformamidase activity / tryptophan catabolic process to kynurenine / 'de novo' NAD biosynthetic process from tryptophan / NAD biosynthetic process / positive regulation of cell growth / hydrolase activity
Similarity search - Function
Kynurenine formamidase, vertebrates/fungi-type / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Kynurenine formamidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution
Authors: Arndt, J.W. / Schwarzenbacher, R. / Page, R. / Abdubek, P. / Ambing, E. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / ...Authors: Arndt, J.W. / Schwarzenbacher, R. / Page, R. / Abdubek, P. / Ambing, E. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Hornsby, M. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Jaroszewski, L. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Nigoghossian, E. / Ouyang, J. / Peti, W.S. / Quijano, K. / Reyes, R. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / White, A. / Wolf, G. / Xu, Q. / Zagnitko, O. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionMay 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE CLONING ARTIFACT. THE CONSTRUCT WAS PCR AMPLIFIED WITH TAQ POLYMERASE. SEQUENCING OF THE ...SEQUENCE CLONING ARTIFACT. THE CONSTRUCT WAS PCR AMPLIFIED WITH TAQ POLYMERASE. SEQUENCING OF THE CLONED CONSTRUCT INDICATED THAT VAL IN POSITION 161 WAS MUTATED TO ILE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative serine hydrolase
B: putative serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9625
Polymers63,7422
Non-polymers2203
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-7 kcal/mol
Surface area20610 Å2
MethodPISA
2
A: putative serine hydrolase
hetero molecules

B: putative serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9625
Polymers63,7422
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2070 Å2
ΔGint-14 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.967, 85.959, 70.479
Angle α, β, γ (deg.)90.00, 97.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative serine hydrolase /


Mass: 31871.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ydr428c / Production host: Escherichia coli (E. coli) / References: UniProt: Q04066
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 1.93 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 16.00% PEG MME 2000, 0.10M HEPES, 0.00M HEPES_Na, 5% Glycerol , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9464, 0.979326, 0.979179
DetectorType: ADSC / Detector: CCD / Date: Nov 13, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94641
20.9793261
30.9791791
ReflectionResolution: 1.85→50 Å / Num. obs: 42225 / % possible obs: 99.77 % / Redundancy: 3.89 % / Biso Wilson estimate: 27.53 Å2 / Rsym value: 0.069 / Net I/σ(I): 17.88
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.57 % / Mean I/σ(I) obs: 3.57 / Num. unique all: 4159 / Rsym value: 0.343 / % possible all: 98.39

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→37.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.233 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. NON-ROTOMERS: LEU 156 AND LEU 160 (MOLECULE A AND B).
RfactorNum. reflection% reflectionSelection details
Rfree0.1894 2060 5 %RANDOM
Rwork0.14292 ---
obs0.14523 39479 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.02 Å2
2--0.07 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 13 454 4600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224282
X-RAY DIFFRACTIONr_bond_other_d0.0030.023868
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9555801
X-RAY DIFFRACTIONr_angle_other_deg0.90939055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42225.271203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32815782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.531516
X-RAY DIFFRACTIONr_chiral_restr0.110.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
X-RAY DIFFRACTIONr_nbd_refined0.2150.2955
X-RAY DIFFRACTIONr_nbd_other0.1810.24037
X-RAY DIFFRACTIONr_nbtor_other0.0880.22356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2424
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.231
X-RAY DIFFRACTIONr_mcbond_it1.4961.52801
X-RAY DIFFRACTIONr_mcbond_other0.3731.51030
X-RAY DIFFRACTIONr_mcangle_it1.65924214
X-RAY DIFFRACTIONr_scbond_it3.07231876
X-RAY DIFFRACTIONr_scangle_it4.2474.51587
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 127 4.92 %
Rwork0.174 2453 -
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)
10.6720.1523-0.01720.5367-0.05871.179-0.0142-0.0893-0.03630.0354-0.0006-0.06540.0542-0.01670.0147-0.1074-0.0010.0052-0.2667-0.0023-0.2105-8.68531.71473.862
20.93650.04870.03720.80110.13411.73410.05030.131-0.0146-0.04910.0193-0.0483-0.0038-0.0144-0.0696-0.1262-0.01110.013-0.24140.0089-0.20045.07537.6141.835
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA7 - 26119 - 273
22BB10 - 26122 - 273

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