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- PDB-4mmi: Crystal structure of heparan sulfate lyase HepC mutant from Pedob... -

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Basic information

Entry
Database: PDB / ID: 4mmi
TitleCrystal structure of heparan sulfate lyase HepC mutant from Pedobacter heparinus
ComponentsHeparinase III protein
KeywordsLYASE / alpha/alpha barrel anti-parallel beta-sheet / heparinase
Function / homology
Function and homology information


heparin-sulfate lyase / heparin-sulfate lyase activity / heparan sulfate proteoglycan catabolic process / periplasmic space
Similarity search - Function
Heparin-sulfate lyase, N-terminal / : / Heparinase II/III N-terminus / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase ...Heparin-sulfate lyase, N-terminal / : / Heparinase II/III N-terminus / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Heparin-sulfate lyase
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMaruyama, Y. / Nakamichi, Y. / Mikami, B. / Murata, K. / Hashimoto, W.
CitationJournal: Biochemistry / Year: 2014
Title: Crystal Structure of Pedobacter heparinus Heparin Lyase Hep III with the Active Site in a Deep Cleft
Authors: Hashimoto, W. / Maruyama, Y. / Nakamichi, Y. / Mikami, B. / Murata, K.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 8, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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

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Assembly

Deposited unit
A: Heparinase III protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4223
Polymers74,3411
Non-polymers802
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.674, 102.897, 149.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heparinase III protein


Mass: 74341.477 Da / Num. of mol.: 1 / Fragment: UNP residues 25-695 / Mutation: I29V, L659S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter heparinus (bacteria) / Gene: HepC / Production host: Escherichia coli (E. coli) / References: UniProt: Q59289, heparin-sulfate lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27715 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 38.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMH

4mmh


Resolution: 2.4→35.94 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.942 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24907 1389 5 %RANDOM
Rwork0.20493 ---
obs0.20719 26271 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.728 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å2-0 Å2-0 Å2
2--3.42 Å2-0 Å2
3----6.96 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 2 61 5264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195346
X-RAY DIFFRACTIONr_bond_other_d0.0010.024962
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.9297246
X-RAY DIFFRACTIONr_angle_other_deg0.716311395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64124.235281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40215895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.631531
X-RAY DIFFRACTIONr_chiral_restr0.0650.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021351
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 89 -
Rwork0.288 1880 -
obs--98.11 %

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