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- PDB-1z9n: X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ... -

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Basic information

Entry
Database: PDB / ID: 1z9n
TitleX-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi with haem bound at the dimer interface
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / CU-ZN SOD / SOD / HAEM
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHaemophilus ducreyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDjinovic Carugo, K. / Toeroe, I.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural basis of heme binding in the Cu,Zn superoxide dismutase from Haemophilus ducreyi.
Authors: Toro, I. / Petrutz, C. / Pacello, F. / D'Orazio, M. / Battistoni, A. / Djinovic-Carugo, K.
History
DepositionApr 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 26, 2011Group: Database references
Revision 1.4Aug 23, 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 / struct_site
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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,23214
Polymers76,4834
Non-polymers1,74910
Water19,4921082
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1167
Polymers38,2422
Non-polymers8745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-28 kcal/mol
Surface area14090 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1167
Polymers38,2422
Non-polymers8745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-28 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.320, 65.900, 69.540
Angle α, β, γ (deg.)66.59, 89.87, 76.03
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
DetailsThe biological assembly is a dimer in the asymmetric unit

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Components

#1: Protein
Superoxide dismutase [Cu-Zn] / E.C.1.15.1.1


Mass: 19120.766 Da / Num. of mol.: 4 / Fragment: MATURE PROTEIN WITH HAEM BOUND
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Gene: sodC / Production host: Escherichia coli (E. coli) / References: UniProt: Q59452, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1082 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 8000, sodium cacodylate, sodium acetate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 12, 2001 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→19.5 Å / Num. all: 88269 / Num. obs: 88269 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 20.284 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 10.83
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 2.99 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.53 / Num. unique all: 13302 / Rsym value: 0.278 / % possible all: 88.6

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Processing

Software
NameVersionClassification
XDSdata reduction
AMoREphasing
REFMAC5.2refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2APS

2aps


Resolution: 1.5→19.5 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19332 4488 5 %RANDOM
Rwork0.15651 ---
all0.15834 85257 --
obs0.15834 85257 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.838 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.38 Å2-0.16 Å2
2--0.23 Å2-0.28 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 0 94 1082 5820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214953
X-RAY DIFFRACTIONr_bond_other_d0.0010.024315
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9946707
X-RAY DIFFRACTIONr_angle_other_deg0.801310163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86524.948194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73515778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.247158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02840
X-RAY DIFFRACTIONr_nbd_refined0.2010.2905
X-RAY DIFFRACTIONr_nbd_other0.1850.24317
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.22805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2757
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1390.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2770.286
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.81623914
X-RAY DIFFRACTIONr_mcbond_other0.27721280
X-RAY DIFFRACTIONr_mcangle_it2.16844921
X-RAY DIFFRACTIONr_scbond_it3.39342174
X-RAY DIFFRACTIONr_scangle_it4.3361782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.224 317
Rwork0.192 6015
obs-6332

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