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- PDB-3ngg: X-ray Structure of Omwaprin -

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Basic information

Entry
Database: PDB / ID: 3ngg
TitleX-ray Structure of Omwaprin
ComponentsOmwaprin-a
KeywordsANTIBIOTIC / Venom protein / racemic protein crystallography / Direct methods
Function / homology
Function and homology information


venom-mediated disruption of cell wall in another organism / peptidase inhibitor activity / defense response to bacterium / extracellular region
Similarity search - Function
Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesOxyuranus microlepidotus (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.33 Å
AuthorsBanigan, J.R. / Mandal, K. / Sawaya, M.R. / Thammavongsa, V. / Hendrickx, A.P.A. / Schneewind, O. / Yeates, T.O. / Kent, S.B.H.
CitationJournal: Protein Sci. / Year: 2010
Title: Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography.
Authors: Banigan, J.R. / Mandal, K. / Sawaya, M.R. / Thammavongsa, V. / Hendrickx, A.P. / Schneewind, O. / Yeates, T.O. / Kent, S.B.
History
DepositionJun 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Omwaprin-a
B: Omwaprin-a


Theoretical massNumber of molelcules
Total (without water)11,2432
Polymers11,2432
Non-polymers00
Water2,522140
1
A: Omwaprin-a


Theoretical massNumber of molelcules
Total (without water)5,6221
Polymers5,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Omwaprin-a


Theoretical massNumber of molelcules
Total (without water)5,6221
Polymers5,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.090, 46.558, 39.650
Angle α, β, γ (deg.)90.00, 92.75, 90.00
Int Tables number14
Space group name H-MP121/c1

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Components

#1: Protein/peptide Omwaprin-a / Oxywaprin-a / Oxywaprin


Mass: 5621.564 Da / Num. of mol.: 2 / Fragment: L-Omwaprin / Source method: obtained synthetically / Details: Chemical synthesis / Source: (synth.) Oxyuranus microlepidotus (cobra) / References: UniProt: P83952
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.81 Å3/Da / Density % sol: 31.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 61% Tacsimate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2009
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. all: 35749 / Num. obs: 35749 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 25.5
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.5 / % possible all: 80.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.33→44.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.924 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The structure is from Racemic Protein Crystal where both L- and D- Omwaprin present. The asymmetry unit contains two L-Omwaprin proteins that can be transformed to D-Omwaprin through space ...Details: The structure is from Racemic Protein Crystal where both L- and D- Omwaprin present. The asymmetry unit contains two L-Omwaprin proteins that can be transformed to D-Omwaprin through space group P21/C. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20979 1756 5 %RANDOM
Rwork0.17419 ---
obs0.17602 33231 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.228 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.3 Å2
2---0.19 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.33→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 0 0 140 854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022760
X-RAY DIFFRACTIONr_bond_other_d0.0020.02590
X-RAY DIFFRACTIONr_angle_refined_deg1.9472.0311030
X-RAY DIFFRACTIONr_angle_other_deg2.0331461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.056598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39226.12931
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96715144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.082154
X-RAY DIFFRACTIONr_chiral_restr0.1080.297
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022830
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02114
X-RAY DIFFRACTIONr_mcbond_it3.7011.5486
X-RAY DIFFRACTIONr_mcbond_other3.1251.5182
X-RAY DIFFRACTIONr_mcangle_it5.3322794
X-RAY DIFFRACTIONr_scbond_it5.9863274
X-RAY DIFFRACTIONr_scangle_it7.6164.5233
X-RAY DIFFRACTIONr_rigid_bond_restr3.61331350
X-RAY DIFFRACTIONr_sphericity_free18.023140
X-RAY DIFFRACTIONr_sphericity_bonded8.06531322
LS refinement shellResolution: 1.331→1.366 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 110 -
Rwork0.213 1954 -
obs--77.54 %

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