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- PDB-4z8i: Crystal structure of Branchiostoma belcheri tsingtauense peptidog... -

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Basic information

Entry
Database: PDB / ID: 4z8i
TitleCrystal structure of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3
Componentspeptidoglycan recognition protein 3
KeywordsHYDROLASE / peptidoglycan recognition protein / chitin-binding domain / amidase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / chitin binding / peptidoglycan catabolic process / zinc ion binding
Similarity search - Function
Chitin-binding type-1 domain profile. / Chitin-binding, type 1 / Endochitinase-like superfamily / 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 / Ami_2 / N-acetylmuramoyl-L-alanine amidase ...Chitin-binding type-1 domain profile. / Chitin-binding, type 1 / Endochitinase-like superfamily / 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 / Ami_2 / 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
Peptidoglycan recognition protein 3
Similarity search - Component
Biological speciesBranchiostoma belcheri tsingtauense (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsWang, W.J. / Cheng, W. / Jiang, Y.L. / Luo, M. / Cao, D.D. / Chi, C.B. / Yang, H.B. / Chen, Y. / Zhou, C.Z.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2013CB835300 China
Ministry of Science and Technology of China2014CB910100 China
Hefei Science Center of CAS2015SRG-HSC045 China
Hefei Science Center of CAS2015SRG-HSC046 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
DepositionApr 9, 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptidoglycan recognition protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5162
Polymers25,4501
Non-polymers651
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.206, 77.206, 82.607
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein peptidoglycan recognition protein 3 / BbtPGRP3


Mass: 25450.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma belcheri tsingtauense (invertebrata)
Plasmid: pAcGP67 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A0R4I979*PLUS, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.95 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.2 M Lithium sulfate, 0.1 M Tris-HCl

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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: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 15022 / % possible obs: 99.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
REFMAC5.5refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHT

1oht


Resolution: 2.701→38.603 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.56 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 758 5.05 %Random selection
Rwork0.1717 ---
obs0.1732 14999 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.3 Å2
Refinement stepCycle: LAST / Resolution: 2.701→38.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 1 74 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031741
X-RAY DIFFRACTIONf_angle_d0.8122355
X-RAY DIFFRACTIONf_dihedral_angle_d12.109610
X-RAY DIFFRACTIONf_chiral_restr0.059241
X-RAY DIFFRACTIONf_plane_restr0.003312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7005-2.9090.26171450.20952862X-RAY DIFFRACTION99
2.909-3.20160.23691550.19042855X-RAY DIFFRACTION99
3.2016-3.66460.2131380.1612865X-RAY DIFFRACTION99
3.6646-4.61580.15561620.14252825X-RAY DIFFRACTION99
4.6158-38.60690.20241580.18562834X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -33.8329 Å / Origin y: 11.8014 Å / Origin z: 19.6129 Å
111213212223313233
T0.2498 Å20.0128 Å20.0156 Å2-0.2641 Å2-0.0305 Å2--0.2594 Å2
L0.5592 °20.2768 °20.0178 °2-1.4249 °2-0.9157 °2--1.9759 °2
S0.0362 Å °0.0167 Å °-0.1095 Å °0.0024 Å °-0.0856 Å °-0.0603 Å °0.207 Å °0.1685 Å °0.0512 Å °
Refinement TLS groupSelection details: all

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