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- PDB-3t9g: The crystal structure of family 3 pectate lyase from Caldicellulo... -

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Basic information

Entry
Database: PDB / ID: 3t9g
TitleThe crystal structure of family 3 pectate lyase from Caldicellulosiruptor bescii
ComponentsPectate lyase
KeywordsLYASE / PL3 / parallel beta-helix / pectate lyase
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / hydrolase activity / extracellular region / metal ion binding / membrane
Similarity search - Function
Pectate lyase PlyH/PlyE-like / Pectate lyase / 3-keto-disaccharide hydrolase / 3-keto-alpha-glucoside-1,2-lyase-like domain / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / pectate lyase
Similarity search - Component
Biological speciesCaldicellulosiruptor bescii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: A 1.5 A resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase.
Authors: Alahuhta, M. / Chandrayan, P. / Kataeva, I. / Adams, M.W. / Himmel, M.E. / Lunin, V.V.
History
DepositionAug 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Pectate lyase
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,21927
Polymers42,2662
Non-polymers1,95425
Water9,476526
1
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8539
Polymers21,1331
Non-polymers7208
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,36618
Polymers21,1331
Non-polymers1,23417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Pectate lyase
hetero molecules

A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,21927
Polymers42,2662
Non-polymers1,95425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
Buried area4790 Å2
ΔGint-127 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.514, 146.685, 162.159
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
11B-215-

ACT

21B-403-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pectate lyase


Mass: 21132.855 Da / Num. of mol.: 2 / Fragment: unp residues 268-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (bacteria) / Gene: Athe_1854, Cbes_1854 / Plasmid: pET-45b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9MKT4, pectate lyase

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Non-polymers , 10 types, 551 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium phosphate monobasic, 0.1 M Tris, 50% v/v (+/-)-2-methyl-2,4-pentanediol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 29, 2011 / Details: HELIOS MIRRORS
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 70692 / Num. obs: 70692 / % possible obs: 99.6 % / Redundancy: 6.15 % / Rsym value: 0.0446 / Net I/σ(I): 24.73
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.97 % / Mean I/σ(I) obs: 8.23 / Num. unique all: 12550 / Rsym value: 0.1495 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
SAINTdata reduction
PROTEUM PLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EE6

1ee6


Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.095 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17846 3543 5 %RANDOM
Rwork0.14325 ---
all0.14501 66898 --
obs0.14501 66898 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.68 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 121 526 3600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0223483
X-RAY DIFFRACTIONr_bond_other_d0.0030.022251
X-RAY DIFFRACTIONr_angle_refined_deg2.4221.9714776
X-RAY DIFFRACTIONr_angle_other_deg1.27735624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17727.432148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40315599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.625152
X-RAY DIFFRACTIONr_chiral_restr0.1380.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023998
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02604
X-RAY DIFFRACTIONr_mcbond_it1.3351.52174
X-RAY DIFFRACTIONr_mcbond_other0.4131.5891
X-RAY DIFFRACTIONr_mcangle_it2.19223576
X-RAY DIFFRACTIONr_scbond_it3.29831309
X-RAY DIFFRACTIONr_scangle_it5.0854.51186
LS refinement shellResolution: 1.497→1.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 241 -
Rwork0.198 4770 -
obs-4770 97.09 %

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