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- PDB-5hjh: Dps4 from Nostoc punctiforme in complex with Fe ions -

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Basic information

Entry
Database: PDB / ID: 5hjh
TitleDps4 from Nostoc punctiforme in complex with Fe ions
ComponentsFerritin, Dps family protein
KeywordsMETAL BINDING PROTEIN / metal binding / ferredoxin / oxidative stress
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding
Similarity search - Function
Dps protein family signature 2. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferritin, Dps family protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsHowe, C. / Moparthi, V.K. / Persson, K. / Stensjo, K.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Energy Agency11674-5 Sweden
CitationJournal: To Be Published
Title: Dps4 from Nostoc punctiforme in complex with Fe ions
Authors: Howe, C. / Moparthi, V.K. / Persson, K. / Stensjo, K.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin, Dps family protein
B: Ferritin, Dps family protein
C: Ferritin, Dps family protein
D: Ferritin, Dps family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,25513
Polymers80,5704
Non-polymers6859
Water6,756375
1
A: Ferritin, Dps family protein
B: Ferritin, Dps family protein
C: Ferritin, Dps family protein
D: Ferritin, Dps family protein
hetero molecules

A: Ferritin, Dps family protein
B: Ferritin, Dps family protein
C: Ferritin, Dps family protein
D: Ferritin, Dps family protein
hetero molecules

A: Ferritin, Dps family protein
B: Ferritin, Dps family protein
C: Ferritin, Dps family protein
D: Ferritin, Dps family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,76539
Polymers241,70912
Non-polymers2,05527
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area71180 Å2
ΔGint-618 kcal/mol
Surface area57030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.310, 100.310, 145.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-350-

HOH

21B-375-

HOH

31B-376-

HOH

41B-406-

HOH

51D-310-

HOH

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Components

#1: Protein
Ferritin, Dps family protein / / DNA binding protein from starved cells.


Mass: 20142.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: 102 / Gene: Npun_R5799 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2J981
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% SOKALAN HP 66, 0.1 M HEPES pH 7.0 and 0.2 M NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.88→48.55 Å / Num. obs: 67029 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 32.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.035 / Net I/σ(I): 12.3 / Num. measured all: 288333 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.88-1.954.40.9931.72859165120.6730.52999
7.28-48.553.90.06834.9453611700.9930.03798

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.2data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJF

5hjf


Resolution: 1.88→47.422 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 2004 2.99 %Random
Rwork0.1576 64989 --
obs0.1586 66993 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.19 Å2 / Biso mean: 40.5613 Å2 / Biso min: 23.14 Å2
Refinement stepCycle: final / Resolution: 1.88→47.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 23 375 6063
Biso mean--62.73 46.45 -
Num. residues----709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075796
X-RAY DIFFRACTIONf_angle_d0.9557844
X-RAY DIFFRACTIONf_chiral_restr0.038861
X-RAY DIFFRACTIONf_plane_restr0.0051030
X-RAY DIFFRACTIONf_dihedral_angle_d14.8372087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.88-1.9270.36861400.2839462899
1.927-1.97910.26841400.2618459199
1.9791-2.03740.29191440.2181462899
2.0374-2.10310.24041420.2005461799
2.1031-2.17830.23081420.1856463999
2.1783-2.26550.23411430.17454609100
2.2655-2.36860.23011430.16284614100
2.3686-2.49350.21571440.15884667100
2.4935-2.64970.22071390.16134651100
2.6497-2.85430.18621460.15744662100
2.8543-3.14150.20481450.15794642100
3.1415-3.59590.15811430.15254672100
3.5959-4.52990.1571500.12694680100
4.52990.17441430.1443468999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90070.19490.47930.70960.23121.5589-0.02520.08460.2325-0.0204-0.04450.0199-0.4443-0.00710.07480.45780.0344-0.07360.2390.03420.3854-2.7728-29.4344-12.775
21.45970.45730.68761.03590.45241.7984-0.0570.12610.2273-0.1454-0.0786-0.114-0.2530.24990.11270.3224-0.06710.01370.32480.08910.311515.4272-40.3922-20.9169
30.83480.333-0.2581.4725-0.6441.44-0.0679-0.03870.12850.0928-0.040.1451-0.311-0.43050.0880.32340.1428-0.00730.4256-0.09490.3999-24.51-40.35268.4914
40.93780.5456-0.18851.4459-0.32821.1786-0.0586-0.19010.12740.2585-0.00320.0604-0.2555-0.1050.05440.39880.056-0.01130.3604-0.10480.3027-9.3012-41.822425.1911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:182)A6 - 182
2X-RAY DIFFRACTION2(chain B and resid 6:182)B6 - 182
3X-RAY DIFFRACTION3(chain C and resid 6:182)C6 - 182
4X-RAY DIFFRACTION4(chain D and resid 5:182)D5 - 182

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