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- PDB-7dya: Crystal structure of TmFtn with calcium ions -

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Basic information

Entry
Database: PDB / ID: 7dya
TitleCrystal structure of TmFtn with calcium ions
ComponentsFerritin
KeywordsPROTEIN BINDING / Thermotoga maritima ferritin / Calcium ions
Function / homology
Function and homology information


bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsZhang, X. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: Nat Commun / Year: 2021
Title: Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials.
Authors: Zhang, X. / Liu, Y. / Zheng, B. / Zang, J. / Lv, C. / Zhang, T. / Wang, H. / Zhao, G.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Ferritin
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,46933
Polymers155,2158
Non-polymers1,25425
Water18,3571019
1
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
hetero molecules

A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
hetero molecules

H: Ferritin
B: Ferritin
hetero molecules

H: Ferritin
B: Ferritin
hetero molecules

H: Ferritin
B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)469,40799
Polymers465,64424
Non-polymers3,76375
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation4_655y+1,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_665-x+1,-x+y+1,-z1
Buried area79040 Å2
ΔGint-1255 kcal/mol
Surface area151660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.434, 175.434, 357.421
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

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Components

#1: Protein
Ferritin /


Mass: 19401.840 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 14% 2-Propanol, 70 mM Sodium acetate/ HCl pH 4.6, 140 mM Calcium chloride, 30% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.197→38.584 Å / Num. obs: 107433 / % possible obs: 99.92 % / Redundancy: 6.8 % / CC1/2: 0.992 / Net I/σ(I): 5.97
Reflection shellResolution: 2.197→2.197 Å / Num. unique obs: 10652 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.197→38.584 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 1999 1.86 %
Rwork0.1746 105416 -
obs0.1751 107415 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.79 Å2 / Biso mean: 38.2521 Å2 / Biso min: 19.61 Å2
Refinement stepCycle: final / Resolution: 2.197→38.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10936 0 25 1019 11980
Biso mean--39.3 45.01 -
Num. residues----1312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1971-2.2520.2271410.19927448
2.252-2.31290.23151420.19457464
2.3129-2.38090.21811420.18427485
2.3809-2.45780.22731420.18737466
2.4578-2.54560.21671420.19077488
2.5456-2.64750.2291420.19257499
2.6475-2.7680.21011420.18247467
2.768-2.91390.20871420.16947516
2.9139-3.09630.19121420.17427519
3.0963-3.33530.2311440.187545
3.3353-3.67070.20181430.16297536
3.6707-4.20130.18541440.1657563
4.2013-5.2910.17721430.15537620
5.291-6.30.18371480.17477800

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