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- PDB-7vfc: Crystal structure of cPMO2 -

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Basic information

Entry
Database: PDB / ID: 7vfc
TitleCrystal structure of cPMO2
ComponentscPMO2
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenases
Function / homologyCoagulation Factor XIII; Chain A, domain 1 - #70 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / COPPER (II) ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciescompost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsLiu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31572200 China
CitationJournal: To Be Published
Title: Crystal structure of cPMO2
Authors: Liu, D.
History
DepositionSep 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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: cPMO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7553
Polymers23,5851
Non-polymers1702
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.392, 51.223, 57.133
Angle α, β, γ (deg.)90.000, 99.342, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein cPMO2


Mass: 23584.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) compost metagenome (others) / Production host: Komagataella pastoris (fungus)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 25% PEG3350,0.1 M Tris-HCl, pH8.5,0.2M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.21→29.82 Å / Num. obs: 67508 / % possible obs: 98.81 % / Redundancy: 6.6 % / Biso Wilson estimate: 9.47 Å2 / CC1/2: 0.928 / Net I/σ(I): 9.9
Reflection shellResolution: 1.21→1.254 Å / Num. unique obs: 67522 / CC1/2: 0.928

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H1Z

6h1z


Resolution: 1.21→29.82 Å / SU ML: 0.0895 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 17.2825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1788 3330 4.93 %
Rwork0.1552 64178 -
obs0.1564 67508 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.51 Å2
Refinement stepCycle: LAST / Resolution: 1.21→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 8 320 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461761
X-RAY DIFFRACTIONf_angle_d0.80852424
X-RAY DIFFRACTIONf_chiral_restr0.082267
X-RAY DIFFRACTIONf_plane_restr0.0053322
X-RAY DIFFRACTIONf_dihedral_angle_d3.8028913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.230.19321330.1642593X-RAY DIFFRACTION95.18
1.23-1.250.18841220.15652660X-RAY DIFFRACTION99.07
1.25-1.270.18361350.15272690X-RAY DIFFRACTION99.02
1.27-1.290.18411410.15432635X-RAY DIFFRACTION99.07
1.29-1.310.21621370.15172692X-RAY DIFFRACTION99.26
1.31-1.330.18611460.15062668X-RAY DIFFRACTION99.4
1.33-1.360.19281520.1512655X-RAY DIFFRACTION98.04
1.36-1.390.18371330.13592636X-RAY DIFFRACTION99.18
1.39-1.420.16911240.14152702X-RAY DIFFRACTION99.05
1.42-1.450.16461240.1372674X-RAY DIFFRACTION99.36
1.45-1.490.15011530.14182643X-RAY DIFFRACTION98.87
1.49-1.530.18851600.13542669X-RAY DIFFRACTION99.12
1.53-1.570.15341410.1382688X-RAY DIFFRACTION98.74
1.57-1.620.16141120.14562681X-RAY DIFFRACTION99.08
1.62-1.680.16731380.14732669X-RAY DIFFRACTION99.15
1.68-1.750.18811350.15422707X-RAY DIFFRACTION99.16
1.75-1.830.17461400.15182653X-RAY DIFFRACTION98.69
1.83-1.920.18751420.15212685X-RAY DIFFRACTION99.16
1.92-2.040.18121500.15122645X-RAY DIFFRACTION98.04
2.04-2.20.19081600.15412671X-RAY DIFFRACTION99.16
2.2-2.420.18761440.16192681X-RAY DIFFRACTION99.02
2.42-2.770.17421400.1662668X-RAY DIFFRACTION98.49
2.77-3.490.17621310.15882741X-RAY DIFFRACTION99.41

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