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- PDB-4zxm: Crystal structure of PGRP domain from Branchiostoma belcheri tsin... -

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Basic information

Entry
Database: PDB / ID: 4zxm
TitleCrystal structure of PGRP domain from Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3
ComponentsPGRP domain of peptidoglycan recognition protein 3
KeywordsHYDROLASE / peptidoglycan recognition protein / amidase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / zinc ion binding
Similarity search - Function
Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / Lysozyme-like / Peptidoglycan recognition protein-like / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PGRP domain of peptidoglycan recognition protein 3
Similarity search - Component
Biological speciesBranchiostoma belcheri tsingtauense (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, W.J. / Cheng, W. / Jiang, Y.L. / Yu, H.M. / Luo, M.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2013CB835300 China
Ministry of Science and Technology of China2014CB910100 China
CitationJournal: Plos One / Year: 2015
Title: Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain
Authors: Wang, W.J. / Cheng, W. / Luo, M. / Yan, Q. / Yu, H.M. / Li, Q. / Cao, D.D. / Huang, S. / Xu, A. / Mariuzza, R.A. / Chen, Y. / Zhou, C.Z.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PGRP domain of peptidoglycan recognition protein 3


Theoretical massNumber of molelcules
Total (without water)27,5691
Polymers27,5691
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7420 Å2
Unit cell
Length a, b, c (Å)79.596, 79.596, 82.262
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

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Components

#1: Protein PGRP domain of peptidoglycan recognition protein 3


Mass: 27569.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma belcheri tsingtauense (invertebrata)
Plasmid: 2BT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0R4I988*PLUS, N-acetylmuramoyl-L-alanine amidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThis sequence has already been submitted to GenBank and accession number is KR136228.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.8 M Sodium Chloride, 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97886 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 7646 / % possible obs: 98.7 % / Redundancy: 3.1 % / Net I/σ(I): 8.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHT

1oht


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.028 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21948 350 4.6 %RANDOM
Rwork0.19653 ---
obs0.19767 7285 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.65 Å20 Å2
2--1.31 Å2-0 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 0 19 1271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191282
X-RAY DIFFRACTIONr_bond_other_d0.0010.021172
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9261737
X-RAY DIFFRACTIONr_angle_other_deg0.72932686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21122.67956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59515198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8691510
X-RAY DIFFRACTIONr_chiral_restr0.0680.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021491
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02321
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_it2.3895.67659
X-RAY DIFFRACTIONr_mcbond_other2.3885.671658
X-RAY DIFFRACTIONr_mcangle_it4.1928.504822
X-RAY DIFFRACTIONr_mcangle_other4.1898.502823
X-RAY DIFFRACTIONr_scbond_it2.6865.848623
X-RAY DIFFRACTIONr_scbond_other2.6845.846624
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.388.701916
X-RAY DIFFRACTIONr_long_range_B_refined7.92444.5241457
X-RAY DIFFRACTIONr_long_range_B_other7.92144.5261458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 21 -
Rwork0.267 534 -
obs--98.4 %

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