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- PDB-6ldg: Crystal structure of the Zn-directed tetramer of the engineered c... -

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Basic information

Entry
Database: PDB / ID: 6ldg
TitleCrystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96I AB5
Componentsengineered cyt cb 562 variant, C96I AB
KeywordsELECTRON TRANSPORT / Artificial enzyme / Metallohydrolase / Directed evolution / METAL BINDING PROTEIN
Function / homologyHEME C
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsSong, W.J. / Yu, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2019R1C1C1003863 Korea, Republic Of
CitationJournal: Chem Sci / Year: 2021
Title: Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes.
Authors: Yu, J. / Yang, J. / Seok, C. / Song, W.J.
History
DepositionNov 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: engineered cyt cb 562 variant, C96I AB
C: engineered cyt cb 562 variant, C96I AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,47915
Polymers23,6642
Non-polymers1,81413
Water3,495194
1
A: engineered cyt cb 562 variant, C96I AB
C: engineered cyt cb 562 variant, C96I AB
hetero molecules

A: engineered cyt cb 562 variant, C96I AB
C: engineered cyt cb 562 variant, C96I AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,95830
Polymers47,3294
Non-polymers3,62926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area13580 Å2
ΔGint-642 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.723, 53.723, 250.757
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-206-

ZN

21A-369-

HOH

31C-324-

HOH

41C-401-

HOH

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein engineered cyt cb 562 variant, C96I AB


Mass: 11832.235 Da / Num. of mol.: 2 / Fragment: variant, C96I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 207 molecules

#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 100 mM HEPES pH 7.5, 200 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.98→28.38 Å / Num. obs: 15931 / % possible obs: 99.8 % / Redundancy: 40 % / Rsym value: 0.129 / Net I/σ(I): 105.8
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 40.2 % / Num. unique obs: 760 / Rsym value: 0.323 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQ6

3iq6


Resolution: 1.98→28.38 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.352 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.164
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 769 5 %RANDOM
Rwork0.1679 ---
obs0.1706 14722 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.06 Å2 / Biso mean: 22.766 Å2 / Biso min: 7.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.98→28.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 97 194 1949
Biso mean--14.56 29.9 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131800
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171586
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.7252454
X-RAY DIFFRACTIONr_angle_other_deg1.4651.6423690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.47625.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29215296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.691154
X-RAY DIFFRACTIONr_chiral_restr0.0810.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022046
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02344
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 59 -
Rwork0.185 1044 -
all-1103 -
obs--100 %

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