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- PDB-7y74: Apostichopus japonicus ferritin mutant-D129A/E132A -

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Basic information

Entry
Database: PDB / ID: 7y74
TitleApostichopus japonicus ferritin mutant-D129A/E132A
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / ion binding / ferroxidase activity
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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 speciesApostichopus japonicus (Japanese sea cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsWu, Y. / Ming, T.H. / Su, X.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)41676159 China
CitationJournal: To Be Published
Title: Apostichopus japonicus ferritin mutant-D129A/E132A
Authors: Wu, Y.
History
DepositionJun 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,95860
Polymers239,59912
Non-polymers3,35948
Water29,4731636
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,916120
Polymers479,19724
Non-polymers6,71996
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area101200 Å2
ΔGint-1503 kcal/mol
Surface area137250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.830, 130.950, 122.620
Angle α, β, γ (deg.)90.000, 119.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-355-

HOH

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Components

#1: Protein
Ferritin /


Mass: 19966.545 Da / Num. of mol.: 12 / Mutation: D129A,E132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apostichopus japonicus (Japanese sea cucumber)
Gene: BSL78_19566 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2QJV4, ferroxidase
#2: Chemical...
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1636 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Cadmium sulfate hydrate, 0.1 M HEPES pH 7.5, 1.0 M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 182173 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.034 / Rrim(I) all: 0.064 / Χ2: 0.864 / Net I/σ(I): 8.6 / Num. measured all: 617526
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.013.10.40283070.8650.2660.4840.91890.7
2.01-2.053.40.35390500.9160.2210.4170.90799.1
2.05-2.093.40.28891160.9350.1810.3410.91899.5
2.09-2.133.40.2591350.950.1580.2970.94999.4
2.13-2.183.40.21291090.9590.1340.2510.94599.4
2.18-2.233.40.20990960.9660.1330.2480.9699.3
2.23-2.293.30.18391510.9610.1190.2191.09399.4
2.29-2.353.20.14190680.9780.0930.170.99299.5
2.35-2.423.50.12792200.9810.0790.151.04999.8
2.42-2.493.50.11291440.9840.070.1320.97999.8
2.49-2.583.50.09591570.9890.0590.1120.91499.7
2.58-2.693.40.0891290.9910.050.0940.88599.8
2.69-2.813.20.06891730.9920.0440.0810.87499.7
2.81-2.963.40.05591390.9940.0350.0660.84499.3
2.96-3.143.50.04791710.9950.0290.0560.83399.4
3.14-3.393.50.0491580.9960.0250.0470.76699.8
3.39-3.733.30.03591970.9970.0230.0420.75299.4
3.73-4.263.60.0391750.9970.0190.0360.63499.6
4.26-5.373.40.02891990.9970.0180.0340.56699.4
5.37-503.40.02992790.9970.0190.0350.54198.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WPN

5wpn


Resolution: 1.98→47.91 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.326 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 8970 5 %RANDOM
Rwork0.1761 ---
obs0.1783 171839 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.36 Å2 / Biso mean: 27.793 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.98→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16305 0 47 1636 17988
Biso mean--25.81 36.82 -
Num. residues----2046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01416613
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714787
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.6522346
X-RAY DIFFRACTIONr_angle_other_deg1.0471.64334603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6452033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90123.957930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.201153004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6871572
X-RAY DIFFRACTIONr_chiral_restr0.0810.22084
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023124
LS refinement shellResolution: 1.981→2.032 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 625 -
Rwork0.209 10781 -
all-11406 -
obs--84.56 %

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