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- PDB-1r76: Structure of a pectate lyase from Azospirillum irakense -

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Basic information

Entry
Database: PDB / ID: 1r76
TitleStructure of a pectate lyase from Azospirillum irakense
Componentspectate lyase
KeywordsLYASE / a-helical structure
Function / homology
Function and homology information


Pectic acid lyase / Pectic acid lyase / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
: / ISOPROPYL ALCOHOL / Pectate lyase
Similarity search - Component
Biological speciesAzospirillum irakense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsNovoa de Armas, H. / Verboven, C. / De Ranter, C. / Desair, J. / Vande Broek, A. / Vanderleyden, J. / Rabijns, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Azospirillum irakense pectate lyase displays a toroidal fold.
Authors: Novoa De Armas, H. / Verboven, C. / De Ranter, C. / Desair, J. / Vande Broek, A. / Vanderleyden, J. / Rabijns, A.
History
DepositionOct 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2168
Polymers44,5521
Non-polymers6657
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.374, 85.374, 231.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1249-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein pectate lyase


Mass: 44551.680 Da / Num. of mol.: 1 / Fragment: Residues 25-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum irakense (bacteria) / Gene: pelA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X592, pectate lyase

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Non-polymers , 5 types, 261 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 54.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2M ammonium sulfate, Hepes, isopropanol, PEG 4000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.991880, 1.010719, 0.918407
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 14, 2001
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.991881
21.0107191
30.9184071
ReflectionResolution: 2.65→25 Å / Num. all: 14838 / Num. obs: 12504 / % possible obs: 82 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.65→2.7 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→21.75 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 225643.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1445 10.2 %RANDOM
Rwork0.198 ---
obs0.198 14117 92.7 %-
all-14117 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9134 Å2 / ksol: 0.34468 e/Å3
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å211.7 Å20 Å2
2--3.14 Å20 Å2
3----6.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.65→21.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 30 254 3247
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 227 10.4 %
Rwork0.242 1949 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GOL_XPLOR_PARAMGOL_XPLOR_TOP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5IPA_XPLOR_PARAMIPA_XPLOR_TOP.TOP

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