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- PDB-6lp5: Structure of Sinonovacula constricta ferritin -

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Basic information

Entry
Database: PDB / ID: 6lp5
TitleStructure of Sinonovacula constricta ferritin
ComponentsFerritin
KeywordsOXIDOREDUCTASE / Sinonovacula constricta / marine invertebrate / ferritin / metal binding sites / STRUCTURAL PROTEIN
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, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / HEXANE-1,6-DIOL / Ferritin
Similarity search - Component
Biological speciesSinonovacula constricta (Chinese razor clam)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSu, X.R. / Ming, T.H. / Su, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)41676159 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystallographic characterization of ferritin from Sinonovacula constricta.
Authors: Su, C. / Ming, T. / Wu, Y. / Jiang, Q. / Huan, H. / Lu, C. / Zhou, J. / Li, Y. / Song, H. / Su, X.
History
DepositionJan 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,07427
Polymers118,4646
Non-polymers1,60921
Water15,943885
1
A: Ferritin
B: Ferritin
C: Ferritin
E: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
E: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
E: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
E: Ferritin
hetero molecules

D: Ferritin
F: Ferritin
hetero molecules

D: Ferritin
F: Ferritin
hetero molecules

D: Ferritin
F: Ferritin
hetero molecules

D: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,294108
Polymers473,85824
Non-polymers6,43684
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_554x+1/2,y+1/2,z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation7_554-y+1/2,x+1/2,z-1/21
crystal symmetry operation8_554y+1/2,-x+1/2,z-1/21
Buried area99890 Å2
ΔGint-972 kcal/mol
Surface area140690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.510, 154.510, 129.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Ferritin /


Mass: 19744.078 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinonovacula constricta (Chinese razor clam)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D2JIV0, ferroxidase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 885 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1 uL of protein (10 mg/mL, 25 mM Tris-HCl, 150 mM NaCl, pH 8.0), 1 uL precipitant solution (1.0 M 1,6-hexanediol, 0.01 M cobalt (2+) chloride hexahydrate, 0.1 M sodium acetate trihydrate pH 4.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.98→109.26 Å / Num. obs: 697312 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.98 / Net I/σ(I): 38.5
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 104802 / CC1/2: 0.98
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BG7

1bg7


Resolution: 1.98→109.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.598 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 5243 5 %RANDOM
Rwork0.1634 ---
obs0.1654 99517 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.65 Å2 / Biso mean: 24.508 Å2 / Biso min: 6.37 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.98→109.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8218 0 70 885 9173
Biso mean--48.09 32.17 -
Num. residues----1020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0199235
X-RAY DIFFRACTIONr_bond_other_d0.0040.028585
X-RAY DIFFRACTIONr_angle_refined_deg2.1841.95712467
X-RAY DIFFRACTIONr_angle_other_deg1.3319911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46451180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43525.433508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.644151744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1081551
X-RAY DIFFRACTIONr_chiral_restr0.1640.21242
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211027
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022185
LS refinement shellResolution: 1.984→2.035 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 390 -
Rwork0.151 7284 -
all-7674 -
obs--99.15 %

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