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- PDB-2g4l: Anomalous substructure of hydroxynitrile lyase -

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Basic information

Entry
Database: PDB / ID: 2g4l
TitleAnomalous substructure of hydroxynitrile lyase
Components(S)-acetone-cyanohydrin lyase
KeywordsLYASE / anomalous substructure of hydroxynitrile lyase
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.84 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Remark 999SEQUENCE RESIDUE (A CME 94 ) AND RESIDUE (A GLU 95 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.78.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (S)-acetone-cyanohydrin lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8547
Polymers29,3391
Non-polymers5166
Water3,261181
1
A: (S)-acetone-cyanohydrin lyase
hetero molecules

A: (S)-acetone-cyanohydrin lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,70914
Polymers58,6772
Non-polymers1,03212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3620 Å2
ΔGint-142 kcal/mol
Surface area19540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.090, 106.050, 128.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

21A-483-

HOH

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Components

#1: Protein (S)-acetone-cyanohydrin lyase / S-hydroxynitrile lyase / S-hydroxynitrilase / Oxynitrilase


Mass: 29338.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hevea brasiliensis (rubber tree) / References: UniProt: P52704, EC: 4.1.2.39
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#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.: 181 / 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: 2.73 Å3/Da / Density % sol: 54.88 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 28295 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.211 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE (A CME 94 ) AND RESIDUE (A GLU 95 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.78.
RfactorNum. reflection% reflectionSelection details
Rfree0.19654 600 2.1 %RANDOM
Rwork0.17686 ---
obs0.17728 27695 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 26 181 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222194
X-RAY DIFFRACTIONr_bond_other_d0.0010.021958
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9862975
X-RAY DIFFRACTIONr_angle_other_deg1.67834607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94125.25897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25215388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.237154
X-RAY DIFFRACTIONr_chiral_restr0.10.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022365
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02418
X-RAY DIFFRACTIONr_nbd_refined0.2720.2426
X-RAY DIFFRACTIONr_nbd_other0.190.21931
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21045
X-RAY DIFFRACTIONr_nbtor_other0.0850.21145
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0460.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.210
X-RAY DIFFRACTIONr_mcbond_it1.1741.51680
X-RAY DIFFRACTIONr_mcbond_other0.2651.5531
X-RAY DIFFRACTIONr_mcangle_it1.5342.52110
X-RAY DIFFRACTIONr_scbond_it4.16251070
X-RAY DIFFRACTIONr_scangle_it5.44310864
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 42 -
Rwork0.349 2022 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: 13.6001 Å / Origin y: 43.7535 Å / Origin z: 14.8506 Å
111213212223313233
T-0.0871 Å2-0.0126 Å2-0.0117 Å2--0.0747 Å20.0004 Å2---0.1158 Å2
L0.8699 °2-0.0983 °2-0.0536 °2-0.9684 °2-0.0431 °2--0.8998 °2
S0.01 Å °-0.0858 Å °0.0084 Å °0.0828 Å °-0.003 Å °0.0256 Å °-0.0046 Å °-0.0329 Å °-0.0071 Å °

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