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- PDB-8vc8: Crystal structure of heme-loaded design: HEM_3.C9 -

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Basic information

Entry
Database: PDB / ID: 8vc8
TitleCrystal structure of heme-loaded design: HEM_3.C9
ComponentsHEM_3.C9
KeywordsDE NOVO PROTEIN / de novo design / RFdiffusion / AlphaFold2 / RoseTTAFold
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKalvet, I. / Bera, A.K. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2024
Title: Generalized biomolecular modeling and design with RoseTTAFold All-Atom.
Authors: Krishna, R. / Wang, J. / Ahern, W. / Sturmfels, P. / Venkatesh, P. / Kalvet, I. / Lee, G.R. / Morey-Burrows, F.S. / Anishchenko, I. / Humphreys, I.R. / McHugh, R. / Vafeados, D. / Li, X. / ...Authors: Krishna, R. / Wang, J. / Ahern, W. / Sturmfels, P. / Venkatesh, P. / Kalvet, I. / Lee, G.R. / Morey-Burrows, F.S. / Anishchenko, I. / Humphreys, I.R. / McHugh, R. / Vafeados, D. / Li, X. / Sutherland, G.A. / Hitchcock, A. / Hunter, C.N. / Kang, A. / Brackenbrough, E. / Bera, A.K. / Baek, M. / DiMaio, F. / Baker, D.
History
DepositionDec 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEM_3.C9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8523
Polymers22,1401
Non-polymers7132
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.987, 39.622, 119.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein HEM_3.C9


Mass: 22139.631 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
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: 1.87 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3.2M Ammonium Sulfate, 0.1M Citrate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 1.8→28.06 Å / Num. obs: 16611 / % possible obs: 95.57 % / Redundancy: 4.3 % / Biso Wilson estimate: 27.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.05 / Net I/σ(I): 8.84
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 1242 / CC1/2: 0.792 / Rpim(I) all: 0.792 / % possible all: 88.59

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.06 Å / SU ML: 0.2149 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 23.8053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 1650 9.93 %
Rwork0.1893 14961 -
obs0.1937 16611 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 48 62 1610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01541576
X-RAY DIFFRACTIONf_angle_d1.39512140
X-RAY DIFFRACTIONf_chiral_restr0.0806238
X-RAY DIFFRACTIONf_plane_restr0.0094272
X-RAY DIFFRACTIONf_dihedral_angle_d16.5229595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.34091200.32181122X-RAY DIFFRACTION88.59
1.85-1.910.31511230.27331180X-RAY DIFFRACTION91.31
1.91-1.980.28361360.2441187X-RAY DIFFRACTION92.39
1.98-2.060.30641220.21381162X-RAY DIFFRACTION92.11
2.06-2.150.26391400.19431214X-RAY DIFFRACTION94.22
2.15-2.270.23931390.17151256X-RAY DIFFRACTION97.28
2.27-2.410.20971340.17091264X-RAY DIFFRACTION97.63
2.41-2.60.20191470.17971257X-RAY DIFFRACTION97.23
2.6-2.860.26561460.18831296X-RAY DIFFRACTION98.77
2.86-3.270.23071370.19111293X-RAY DIFFRACTION98.28
3.27-4.120.21581490.17541317X-RAY DIFFRACTION99.19
4.12-28.060.21031570.17981413X-RAY DIFFRACTION99.05
Refinement TLS params.Method: refined / Origin x: 1.80165093914 Å / Origin y: 16.1135710669 Å / Origin z: 15.0080262229 Å
111213212223313233
T0.176866276645 Å2-0.00563040535821 Å2-0.0114338570884 Å2-0.136782004826 Å20.00741853135342 Å2--0.159335922583 Å2
L2.54940099574 °20.439848701911 °2-0.191384742697 °2-1.05283559076 °20.202308969776 °2--1.77727752421 °2
S0.0111928944683 Å °0.104441932503 Å °0.0867616738961 Å °0.0299788756694 Å °0.0102185416888 Å °-0.030380682659 Å °-0.0988396681107 Å °0.0682022590325 Å °-0.00481106268642 Å °
Refinement TLS groupSelection details: all

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