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- PDB-2x3h: COLIPHAGE K5A LYASE -

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Basic information

Entry
Database: PDB / ID: 2x3h
TitleCOLIPHAGE K5A LYASE
ComponentsK5 LYASE
KeywordsLYASE / BACTERIOPHAGE / GLYCOSAMINOGLYCAN
Function / homology
Function and homology information


virus tail, fiber / lyase activity
Similarity search - Function
Chaperone of endosialidase / Intramolecular chaperone auto-processing domain / Intramolecular chaperone auto-processing (ICA) domain profile. / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / K5 lyase / K5 lyase
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE K1-5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsThompson, J.E. / Pourhossein, M. / Goldrick, M. / Hudson, T. / Derrick, J.P. / Roberts, I.S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The K5 Lyase Kfla Combines a Viral Tail Spike Structure with a Bacterial Polysaccharide Lyase Mechanism.
Authors: Thompson, J.E. / Pourhossein, M. / Waterhouse, A. / Hudson, T. / Goldrick, M. / Derrick, J.P. / Roberts, I.S.
History
DepositionFeb 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.5May 8, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: K5 LYASE
B: K5 LYASE
C: K5 LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,08915
Polymers169,1313
Non-polymers95912
Water15,745874
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35210 Å2
ΔGint-167.7 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.530, 130.400, 145.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 5 / Auth seq-ID: 13 - 504 / Label seq-ID: 50 - 541

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(-0.5019, -0.19, -0.8438), (0.1792, 0.9315, -0.3164), (0.8462, -0.31, -0.4335)118.1, 30.88, 139.3
2given(-0.4961, 0.1801, 0.8494), (-0.1917, 0.9314, -0.3095), (-0.8468, -0.3164, -0.4275)-64.6, 36.86, 169.4

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Components

#1: Protein K5 LYASE / K5A LYASE


Mass: 56376.855 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE K1-5 (virus) / Strain: COLIPHAGE K5A / Plasmid: PLYA100 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9AZ47, UniProt: O09496*PLUS, heparin lyase
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 874 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ANOMALIES HAVE BEEN VERIFIED. THERE ARE SOME CONFLICTS BETWEEN THE Q9AZ47 SEQUENCE IN THE ...SEQUENCE ANOMALIES HAVE BEEN VERIFIED. THERE ARE SOME CONFLICTS BETWEEN THE Q9AZ47 SEQUENCE IN THE DATABASE AND THE SEQUENCE USED FOR EXPRESSION OF THE PROTEIN. A CORRECTED SEQUENCE ENTRY WILL BE SUBMITTED TO THE SEQUENCE DATABASE IN DUE COURSE BY THE DEPOSITOR OF THIS ENTRY.

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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: 1.97 Å3/Da / Density % sol: 0.38 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALS WERE GROWN FROM HANGING DROPS; DROPS WERE FORMED BY MIXING 1UL OF 5.2 MG/ML HIS-KFLA IN 20MM TRISHCL (PH 8.0), 50MM NACL, 5% (V/V) GLYCEROL WITH AN EQUAL VOLUME OF WELL SOLUTION ...Details: CRYSTALS WERE GROWN FROM HANGING DROPS; DROPS WERE FORMED BY MIXING 1UL OF 5.2 MG/ML HIS-KFLA IN 20MM TRISHCL (PH 8.0), 50MM NACL, 5% (V/V) GLYCEROL WITH AN EQUAL VOLUME OF WELL SOLUTION CONTAINING 0.2M KBR AND 10% PEG 3350. CRYSTALLIZATION WAS CARRIED OUT AT 20OC.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.95
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.6→42 Å / Num. obs: 173321 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 7.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→97.18 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.375 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20349 8654 5 %RANDOM
Rwork0.17644 ---
obs0.17779 163564 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→97.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10848 0 12 874 11734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02111016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.94314973
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30851491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14324.694441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.031151680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4081557
X-RAY DIFFRACTIONr_chiral_restr0.0910.21749
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028367
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.34903
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.57620
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.51606
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.332
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.550
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0127487
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49311751
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.53923930
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.29533222
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1992medium positional0.220.5
2B1992medium positional0.20.5
3C1992medium positional0.220.5
1A1624loose positional0.445
2B1624loose positional0.495
3C1624loose positional0.535
1A1992medium thermal0.732
2B1992medium thermal0.692
3C1992medium thermal0.592
1A1624loose thermal1.2410
2B1624loose thermal1.110
3C1624loose thermal1.1710
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 668 -
Rwork0.209 11981 -
obs--100 %

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