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- PDB-4b3e: Structure of copper-zinc superoxide dismutase complexed with bica... -

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Basic information

Entry
Database: PDB / ID: 4b3e
TitleStructure of copper-zinc superoxide dismutase complexed with bicarbonate.
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CARBONATE ION / COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsStrange, R.W. / Hough, M.A. / Antonyuk, S.V. / Hasnain, S.S.
CitationJournal: Plos One / Year: 2012
Title: Structural Evidence for a Copper-Bound Carbonate Intermediate in the Peroxidase and Dismutase Activities of Superoxide Dismutase.
Authors: Strange, R.W. / Hough, M.A. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionJul 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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_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_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

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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]
E: SUPEROXIDE DISMUTASE [CU-ZN]
F: SUPEROXIDE DISMUTASE [CU-ZN]
G: SUPEROXIDE DISMUTASE [CU-ZN]
H: SUPEROXIDE DISMUTASE [CU-ZN]
I: SUPEROXIDE DISMUTASE [CU-ZN]
J: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,95845
Polymers159,58810
Non-polymers2,37035
Water28,5901587
1
A: SUPEROXIDE DISMUTASE [CU-ZN]
F: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,48810
Polymers31,9182
Non-polymers5708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-44.1 kcal/mol
Surface area13900 Å2
MethodPISA
2
B: SUPEROXIDE DISMUTASE [CU-ZN]
G: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3929
Polymers31,9182
Non-polymers4747
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-33.4 kcal/mol
Surface area14090 Å2
MethodPISA
3
C: SUPEROXIDE DISMUTASE [CU-ZN]
H: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2958
Polymers31,9182
Non-polymers3786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-36.7 kcal/mol
Surface area14220 Å2
MethodPISA
4
D: SUPEROXIDE DISMUTASE [CU-ZN]
I: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2958
Polymers31,9182
Non-polymers3786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-34.3 kcal/mol
Surface area13840 Å2
MethodPISA
5
E: SUPEROXIDE DISMUTASE [CU-ZN]
J: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,48810
Polymers31,9182
Non-polymers5708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-31.3 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.994, 203.107, 144.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
SUPEROXIDE DISMUTASE [CU-ZN] / SUPEROXIDE DISMUTASE 1 / HSOD1 / CU-ZN SUPEROXIDE DISMUTASE


Mass: 15958.757 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 5 types, 1622 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CO3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1587 / 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: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 7.5
Details: 1 M AMMONIUM SULPHATE, 50 MM TRIS PH 8.0 AND 50 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2007 / Details: MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 124983 / % possible obs: 94.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SOS

1sos


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.871 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21496 6298 5 %RANDOM
Rwork0.17467 ---
obs0.1767 118562 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11100 0 85 1587 12772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911384
X-RAY DIFFRACTIONr_bond_other_d0.0010.027520
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.94915374
X-RAY DIFFRACTIONr_angle_other_deg0.8383.00218494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46151536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.82925.661484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.586151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4321540
X-RAY DIFFRACTIONr_chiral_restr0.0780.21695
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022058
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.148→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 436 -
Rwork0.21 8365 -
obs--95.26 %
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)
10.62770.1846-0.15270.28690.03020.76020.00060.04220.02780.0261-0.02190.03170.0961-0.11820.02140.0997-0.05670.01870.1389-0.01380.0898122.46357.7353.031
20.6614-0.17480.38240.9860.02721.238-0.28990.07040.105-0.02930.01870.0072-0.46280.08480.27120.3531-0.0505-0.15170.01060.0220.0745173.953118.23153.133
30.7449-0.6147-0.18550.8135-0.01640.3461-0.0120.0149-0.0187-0.0048-0.01770.00210.01930.04570.02970.10110.0322-0.00290.11490.0150.0958201.97943.45152.959
41.71940.86940.68931.49860.52720.6655-0.1640.2899-0.0157-0.04660.0682-0.1309-0.16710.17730.09580.0779-0.1028-0.04170.21690.07130.0742176.466149.49752.662
50.18240.17190.04182.9489-0.42080.31810.0298-0.06810.1003-0.3042-0.00510.30650.07480.033-0.02470.10960.0039-0.02940.0539-0.01550.1686125.03687.76347.027
60.74040.1541-0.06540.225-0.00250.3784-0.01060.00280.00410.00420.00430.00230.0354-0.00930.00620.1108-0.00460.00350.1088-0.00430.0976148.85366.6254.197
70.25680.16880.10840.7697-0.01140.5369-0.02760.01860.01380.0169-0.01110.0438-0.05740.03090.03880.12760.0028-0.00740.0913-0.00940.0965169.50690.75454.159
80.6377-0.55220.07540.70620.03660.2472-0.01490.0035-0.0085-0.0104-0.01910.0264-0.0033-0.0010.03410.10520.01620.00650.11120.00220.0982180.26760.77754.259
90.40080.14850.07671.878-0.09980.28080.02090.0094-0.0849-0.04570.00160.1215-0.02570.0513-0.02250.09870.0218-0.00050.06970.00510.1351130.08115.12349.39
100.92680.22190.20160.21350.18420.5915-0.0760.0930.01660.02590.0398-0.0001-0.07170.03480.03620.0845-0.0052-0.01880.14850.010.0812150.37139.8352.269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 156
2X-RAY DIFFRACTION2B1 - 156
3X-RAY DIFFRACTION3C1 - 156
4X-RAY DIFFRACTION4D1 - 156
5X-RAY DIFFRACTION5E1 - 156
6X-RAY DIFFRACTION6F1 - 156
7X-RAY DIFFRACTION7G1 - 156
8X-RAY DIFFRACTION8H1 - 156
9X-RAY DIFFRACTION9J1 - 156
10X-RAY DIFFRACTION10I1 - 156

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