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- PDB-5b0h: CRYSTAL STRUCTURE OF HUMAN LEUKOCYTE CELL-DERIVED CHEMOTAXIN 2 -

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Basic information

Entry
Database: PDB / ID: 5b0h
TitleCRYSTAL STRUCTURE OF HUMAN LEUKOCYTE CELL-DERIVED CHEMOTAXIN 2
ComponentsLeukocyte cell-derived chemotaxin-2
KeywordsMETAL BINDING PROTEIN / CHEMOKINE / M23 METALLOPEPTIDASE FOLD
Function / homology
Function and homology information


skeletal system development / chemotaxis / extracellular space / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Leukocyte cell-derived chemotaxin 2 / Leukocyte cell-derived chemotaxin 2, chordata / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte cell-derived chemotaxin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsZheng, H. / Miyakawa, T. / Sawano, Y. / Tanokura, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure of Human Leukocyte Cell-derived Chemotaxin 2 (LECT2) Reveals a Mechanistic Basis of Functional Evolution in a Mammalian Protein with an M23 Metalloendopeptidase Fold
Authors: Zheng, H. / Miyakawa, T. / Sawano, Y. / Asano, A. / Okumura, A. / Yamagoe, S. / Tanokura, M.
History
DepositionOct 29, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukocyte cell-derived chemotaxin-2
B: Leukocyte cell-derived chemotaxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7235
Polymers29,4962
Non-polymers2273
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-99 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.415, 63.514, 63.976
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 Leukocyte cell-derived chemotaxin-2 / hLECT2


Mass: 14747.893 Da / Num. of mol.: 2 / Fragment: UNP residues 19-151 / Mutation: I40V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LECT2 / Plasmid: PET48B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-GAMI 2(DE3) / References: UniProt: O14960
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONFLICT IS DUE TO NATURAL VARIANT. THE ACCESSION NUMBER OF THIS HUMAN LECT2 GENE IS GENBANK ...THIS CONFLICT IS DUE TO NATURAL VARIANT. THE ACCESSION NUMBER OF THIS HUMAN LECT2 GENE IS GENBANK ACCESSION NO.BC093670.

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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: 2.05 Å3/Da / Density % sol: 39.89 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG8000, 0.2M AMMONIUM SULFATE, 0.1M HEPES / PH range: 7.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 30, 2010
RadiationMonochromator: NUMERICAL LINK TYPE SI 111 DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 18525 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Net I/σ(I): 51.9
Reflection shellResolution: 1.94→2.01 Å / % possible all: 97.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: SAD / Resolution: 1.94→45.07 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.203 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 948 5.1 %RANDOM
Rwork0.177 ---
obs0.179 17531 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2--0.64 Å2-0 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.94→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 7 167 2218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192102
X-RAY DIFFRACTIONr_bond_other_d0.0070.022006
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.962842
X-RAY DIFFRACTIONr_angle_other_deg0.9163.0054620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91123.86488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22215358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3651512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02484
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_it1.5841.5851062
X-RAY DIFFRACTIONr_mcbond_other1.5781.5851061
X-RAY DIFFRACTIONr_mcangle_it2.3442.371324
X-RAY DIFFRACTIONr_mcangle_other2.3452.3711325
X-RAY DIFFRACTIONr_scbond_it2.4521.8591040
X-RAY DIFFRACTIONr_scbond_other2.4431.8581036
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7832.6581512
X-RAY DIFFRACTIONr_long_range_B_refined5.34413.2212337
X-RAY DIFFRACTIONr_long_range_B_other5.19413.0472301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 69 -
Rwork0.174 1228 -
obs--96.79 %

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