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- PDB-1fha: SOLVING THE STRUCTURE OF HUMAN H FERRITIN BY GENETICALLY ENGINEER... -

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Basic information

Entry
Database: PDB / ID: 1fha
TitleSOLVING THE STRUCTURE OF HUMAN H FERRITIN BY GENETICALLY ENGINEERING INTERMOLECULAR CRYSTAL CONTACTS
DescriptorFERRITIN (H-CHAIN) MUTANT (LYS 86 REPLACED BY GLN) (K86Q)
KeywordsMETAL BINDING PROTEIN / IRON STORAGE
Specimen sourceHomo sapiens / human
MethodX-ray diffraction (2.4 Å resolution)
AuthorsArtymiuk, P.J. / Harrison, P.M.
CitationNature, 1991, 349, 541-544

Nature, 1991, 349, 541-544 StrPapers
Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts.
Lawson, D.M. / Artymiuk, P.J. / Yewdall, S.J. / Smith, J.M. / Livingstone, J.C. / Treffry, A. / Luzzago, A. / Levi, S. / Arosio, P. / Cesareni, G. / Thomas, C.D. / Shaw, W.V. / Harrison, P.M.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 20, 1990 / Release: Jul 15, 1992
RevisionDateData content typeGroupProviderType
1.0Jul 15, 1992Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
1.3Nov 16, 2011Structure modelAtomic model
1.4Feb 29, 2012Structure modelDatabase references
Remark 700SHEET THERE IS A STRAND FROM 84 TO 86 THAT FORMS A TENUOUS TWO-STRANDED ANIT-PARALLEL BETA SHEET WITH THE EQUIVALENT STRAND IN A TWO-FOLD RELATED SUBUNIT.

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Assembly

Deposited unit
A: FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3914
Polyers21,2551
Non-polymers1363
Water36020
#1
A: FERRITIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)513,37596
Polyers510,11124
Non-polymers3,26472
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area (Å2)90720
ΔGint (kcal/M)-550
Surface area (Å2)137520
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)184.800, 184.800, 184.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF 4 3 2

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Components

#1: Polypeptide(L)FERRITIN


Mass: 21254.605 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P02794

Cellular component

Molecular function

Biological process

#2: ChemicalChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Formula: Fe
#3: ChemicalChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca
#4: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Formula: H2O
Compound detailsTHE FERROXIDASE CENTER WHICH CATALYSES THE OXIDATION OF FE(II) TO FE(III) INVOLVES THE FOLLOWING RESIDUES: GLU 26, GLU 62, HIS 64, FE 200. COORDINATION CONSIDERATIONS SUGGEST THAT THIS FE IS REALLY A CALCIUM ION IN THIS STRUCTURE.
Sequence detailsTHE FERRITIN SEQUENCE CLONED IN ESCHERICHIA COLI WAS THAT OF HOMO SAPIENS EXCEPT THAT LYS 86 WAS CHANGED TO GLN FOR THE REASON GIVEN IN REMARK 5. RESIDUE NUMBERING WAS CHOSEN TO BE CONSISTENT WITH THE RAT L CHAIN FERRITIN WHICH HAS AN EIGHT RESIDUE INSERTION (RELATIVE TO HUMAN FERRITIN) FROM 162 - 169 (INCLUSIVE). THESE EIGHT RESIDUES ARE NOT PRESENT IN HUMAN H FERRITIN. THUS IN HUMAN H FERRITIN THE RESIDUE NUMBERING GOES DIRECTLY FROM 161 TO 170 BUT NO RESIDUES ARE MISSING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 / Density percent sol: 60.23

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.4 Å / D resolution low: 20 Å / Number obs: 10318 / Number measured all: 54965 / Percent possible obs: 95 / Rmerge I obs: 0.128

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefineDetails: THE STRUCTURE WAS SOLVED BY GENETICALLY ENGINEERING INTERMOLECULAR CRYSTAL CONTACTS FROM THE KNOWN STRUCTURE OF HORSE L CHAIN FERRITIN INTO HUMAN H CHAIN FERRITIN.
Least-squares processR factor obs: 0.205 / Highest resolution: 2.4 Å
Refine hist #LASTHighest resolution: 2.4 Å
Number of atoms included #LASTProtein: 1338 / Nucleic acid: 0 / Ligand: 3 / Solvent: 20 / Total: 1361
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0200.020
X-RAY DIFFRACTIONp_angle_d0.0360.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.025
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0110.020
X-RAY DIFFRACTIONp_chiral_restr0.0380.200
X-RAY DIFFRACTIONp_singtor_nbd0.2100.500
X-RAY DIFFRACTIONp_multtor_nbd0.1960.500
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1360.500
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Least-squares process
*PLUS
R factor obs: 0.205 / Lowest resolution: 20 Å

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