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- PDB-5i4j: Dps4 from Nostoc punctiforme in complex with Zn ions -

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Basic information

Entry
Database: PDB / ID: 5i4j
TitleDps4 from Nostoc punctiforme in complex with Zn ions
ComponentsFerritin, Dps family protein
KeywordsMETAL BINDING PROTEIN / ferritin like
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 / Resolution: 2.394 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: On the trail of iron into Dps4 from N. punctiforme
Authors: Howe, C. / Moparthi, V.K. / Persson, K. / Stensjo, K.
History
DepositionFeb 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id

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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)80,5579
Polymers80,0574
Non-polymers5005
Water1,20767
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)241,67227
Polymers240,17212
Non-polymers1,50015
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 area67590 Å2
ΔGint-789 kcal/mol
Surface area58410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.920, 100.920, 144.270
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-312-

HOH

21B-320-

HOH

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Components

#1: Protein
Ferritin, Dps family protein / Dps4-DNA binding protein from starved cells.


Mass: 20014.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Gene: Npun_R5799 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2J981
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


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


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.65 Å3/Da / Density % sol: 53.57 % / Description: Rod shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% SOKALAN HP 66, 0.1M HEPES pH 7.0 and 0.2M 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: 2.39→48.09 Å / Num. obs: 32761 / % possible obs: 99.8 % / Redundancy: 8.5 % / Biso Wilson estimate: 49.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.045 / Rrim(I) all: 0.131 / Net I/σ(I): 13.9 / Num. measured all: 277574
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.39-2.488.51.681198.5
9.27-48.097.90.034199.4

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Processing

Software
NameVersionClassification
Aimless0.5.2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJF

5hjf


Resolution: 2.394→47.631 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.43
RfactorNum. reflection% reflection
Rfree0.2141 1622 4.96 %
Rwork0.1687 --
obs0.171 32721 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.41 Å2 / Biso mean: 57.7653 Å2 / Biso min: 23.61 Å2
Refinement stepCycle: final / Resolution: 2.394→47.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5656 0 19 67 5742
Biso mean--71.4 51.76 -
Num. residues----708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085787
X-RAY DIFFRACTIONf_angle_d1.0847832
X-RAY DIFFRACTIONf_chiral_restr0.041860
X-RAY DIFFRACTIONf_plane_restr0.0051028
X-RAY DIFFRACTIONf_dihedral_angle_d16.262083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3943-2.46470.32741670.28692518268598
2.4647-2.54430.296850.262226062691100
2.5443-2.63520.29121690.242125732742100
2.6352-2.74070.3308940.239626202714100
2.7407-2.86540.34411520.229125742726100
2.8654-3.01650.28561630.214625512714100
3.0165-3.20540.2774850.212826332718100
3.2054-3.45290.26681560.203725892745100
3.4529-3.80020.22641590.16325612720100
3.8002-4.34980.1941790.134726622741100
4.3498-5.4790.17181600.125425792739100
5.479-47.640.13051530.125226332786100
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)
10.4119-0.14980.02170.80450.09790.5681-0.02840.16560.23420.035-0.0346-0.0289-0.45570.076-0.00050.57340.0153-0.09780.37780.03950.5105-2.6627-29.7255-12.7151
20.5470.0087-0.1560.39650.03560.6524-0.020.25610.1866-0.1377-0.1184-0.0684-0.11870.2576-0.00070.448-0.0975-0.01280.4880.1040.444415.5186-40.733-20.8702
30.6832-0.0293-0.16760.3049-0.02080.8684-0.0032-0.10880.04710.1839-0.11440.125-0.2322-0.4442-0.00220.4220.1631-0.01280.5093-0.08940.4982-24.5055-40.58388.4288
40.16340.070.13190.35070.3150.6443-0.1127-0.19440.04910.25490.02580.0152-0.1955-0.0913-00.52230.086-0.02890.4953-0.08370.4547-9.0544-42.041425.0757
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 6:182)D6 - 182

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