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- PDB-1ooc: Mutations in the T1.5 loop of pectate lyase A -

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Basic information

Entry
Database: PDB / ID: 1ooc
TitleMutations in the T1.5 loop of pectate lyase A
ComponentsPectate lyase A
KeywordsLYASE / parallel beta helix
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding
Similarity search - Function
Pectin lyase family / Pectate lyase / Pectate lyase / Amb_all / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Pectate lyase A / Pectate lyase A
Similarity search - Component
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsDehdashti, S.J. / Doan, C.N. / Chao, K. / Vordtriede, P.B. / Yoder, M.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Effect of mutations in the T1.5 loop of pectate lyase A from Erwinia chrysanthemi EC16.
Authors: Dehdashti, S.J. / Doan, C.N. / Chao, K.L. / Yoder, M.D.
History
DepositionMar 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectate lyase A
B: Pectate lyase A


Theoretical massNumber of molelcules
Total (without water)77,4792
Polymers77,4792
Non-polymers00
Water00
1
A: Pectate lyase A


Theoretical massNumber of molelcules
Total (without water)38,7401
Polymers38,7401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate lyase A


Theoretical massNumber of molelcules
Total (without water)38,7401
Polymers38,7401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.758, 151.205, 50.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer that packs two molecules in the asymmetric unit.

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Components

#1: Protein Pectate lyase A


Mass: 38739.535 Da / Num. of mol.: 2 / Fragment: T1.5 / Mutation: N215S, T217S, S219G, A220S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: PELA / Plasmid: pMDY29 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha
References: UniProt: P29155, UniProt: P0C1A2*PLUS, pectate lyase

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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: 2.39 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000 monomethyl ether (MME), 0.1M MES (2-[N-Morpholino]ethanesulfonic acid), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117.6-20 %PEG5000 MME1reservoir
20.1 MMES1reservoirpH6.5
38.72 mg/mlprotein1drop
42.9-3.3 %PEG5000 MME1drop
50.02 MMES1droppH6.5

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 24, 2003 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 14754 / Num. obs: 14754 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 47.22 Å2 / Rsym value: 0.097 / Net I/σ(I): 23.6
Reflection shellResolution: 2.9→3.08 Å / Mean I/σ(I) obs: 14.6 / Num. unique all: 1511 / Rsym value: 0.273 / % possible all: 81
Reflection
*PLUS
Num. measured all: 128721 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 8.35

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JTA with out residues 215-226

1jta


Resolution: 2.94→29.55 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 743 5.1 %RANDOM
Rwork0.219 ---
all0.219 14701 --
obs0.219 14701 90.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.372263 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.94→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5458 0 0 0 5458
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.93
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.94→3.08 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 103 6.4 %
Rwork0.32 1511 -
obs-1511 58.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. reflection Rfree: 1511 / Rfactor Rfree: 0.2748 / Rfactor Rwork: 0.2195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.665
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93

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