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- PDB-9h4c: Crystal structure of the diheme 4D2 (mutant T19D) with bound Fe(I... -

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Basic information

Entry
Database: PDB / ID: 9h4c
TitleCrystal structure of the diheme 4D2 (mutant T19D) with bound Fe(III) mesoporphyrin IX
Components4D2 (mutant T19D)
KeywordsDE NOVO PROTEIN / 4D2 / Maquette / de novo design
Function / homologyMesoheme
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBarringer, R. / Back, C. / Anderson, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003449/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the diheme 4D2 (mutant T19D) with bound Fe(III) mesoporphyrin IX
Authors: Mellor, C.
History
DepositionOct 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4D2 (mutant T19D)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9073
Polymers12,6661
Non-polymers1,2412
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.187, 81.187, 58.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 4D2 (mutant T19D)


Mass: 12666.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MH0 / Mesoheme


Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.1M DL-Malic acid, pH 7.0

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.98→45.11 Å / Num. obs: 10079 / % possible obs: 100 % / Redundancy: 85.6 % / CC1/2: 0.988 / Rpim(I) all: 0.082 / Net I/σ(I): 11.2
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 504 / CC1/2: 0.402 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→45.11 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.739 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25405 526 5.2 %RANDOM
Rwork0.1954 ---
obs0.19818 9552 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.674 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20 Å2
2--1.71 Å20 Å2
3----3.42 Å2
Refinement stepCycle: 1 / Resolution: 1.98→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 86 6 920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.012938
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4981.8741288
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4475128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.127548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3110157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02716
X-RAY DIFFRACTIONr_gen_planes_other
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_it6.6715.421422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.6719.72524
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.996.044516
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.26865.331546
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.506 52 -
Rwork0.458 713 -
obs--99.87 %

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