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- PDB-4z06: C. bescii Family 3 pectate lyase double mutant K108A/R133A in com... -

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Basic information

Entry
Database: PDB / ID: 4z06
TitleC. bescii Family 3 pectate lyase double mutant K108A/R133A in complex with ALPHA-D-GALACTOPYRANURONIC ACID
ComponentsPectate lyase
KeywordsLYASE / PL3 / PARALLEL BETA-HELIX
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-disaccharide hydrolase / 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
alpha-D-galactopyranuronic acid / pectate lyase
Similarity search - Component
Biological speciesCaldicellulosiruptor bescii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.
Authors: Alahuhta, M. / Taylor, L.E. / Brunecky, R. / Sammond, D.W. / Michener, W. / Adams, M.W. / Himmel, M.E. / Bomble, Y.J. / Lunin, V.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,33917
Polymers44,0402
Non-polymers1,30015
Water8,737485
1
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,84710
Polymers22,0201
Non-polymers8279
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4927
Polymers22,0201
Non-polymers4736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.680, 36.240, 99.820
Angle α, β, γ (deg.)90.00, 132.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Pectate lyase


Mass: 22019.793 Da / Num. of mol.: 2 / Mutation: K375A, R400A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320) (bacteria)
Strain: ATCC BAA-1888 / DSM 6725 / Z-1320 / Gene: Athe_1854 / Production host: Escherichia coli (E. coli) / References: UniProt: B9MKT4, pectate lyase
#3: Sugar ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 498 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.1 and 65.9% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98397 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98397 Å / Relative weight: 1
ReflectionResolution: 1.55→49.8 Å / Num. obs: 49328 / % possible obs: 97.7 % / Redundancy: 13 % / Net I/σ(I): 29.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 5.2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.55→49.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.754 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20045 2565 4.9 %RANDOM
Rwork0.16017 ---
obs0.16228 49328 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.884 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20.04 Å2
2---0.21 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.55→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 0 74 485 3520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193324
X-RAY DIFFRACTIONr_bond_other_d0.0010.023177
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9554552
X-RAY DIFFRACTIONr_angle_other_deg1.3343.0037352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0065446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85527.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56415564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023936
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02716
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4811.3931712
X-RAY DIFFRACTIONr_mcbond_other1.4791.3931711
X-RAY DIFFRACTIONr_mcangle_it2.1352.0842182
X-RAY DIFFRACTIONr_mcangle_other2.1342.0842183
X-RAY DIFFRACTIONr_scbond_it2.4551.6981612
X-RAY DIFFRACTIONr_scbond_other2.4541.6991613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7162.432371
X-RAY DIFFRACTIONr_long_range_B_refined6.10613.2444043
X-RAY DIFFRACTIONr_long_range_B_other5.66312.4243824
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 156 -
Rwork0.217 3566 -
obs--95.68 %

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