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- PDB-3ay2: Crystal structure of Neisserial azurin -

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Basic information

Entry
Database: PDB / ID: 3ay2
TitleCrystal structure of Neisserial azurin
ComponentsLipid modified azurin protein
KeywordsANTITUMOR PROTEIN / ANTIVIRAL PROTEIN / BETA SANDWICH / BACTERIAL PROTEIN / ANTICANCER / ANTI-HIV/AIDS / ANTIPARASITIC ACTIVITY
Function / homology
Function and homology information


cell outer membrane / electron transfer activity / copper ion binding
Similarity search - Function
Azurin / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOchiai, A. / Hashimoto, W. / Yamada, T. / Chakrabarty, A.M. / Murata, K.
CitationJournal: To be Published
Title: Crystal structure of Neisserial Azurin
Authors: Hashimoto, W. / Ochiai, A. / Yamada, T. / Chakrabarty, A.M. / Murata, K.
History
DepositionApr 24, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_ref_seq_dif / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_label_asym_id / _struct_ref_seq_dif.details / _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:
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Assembly

Deposited unit
A: Lipid modified azurin protein
B: Lipid modified azurin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4878
Polymers33,9802
Non-polymers5076
Water2,900161
1
A: Lipid modified azurin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2434
Polymers16,9901
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipid modified azurin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2434
Polymers16,9901
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.513, 77.513, 94.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Lipid modified azurin protein


Mass: 16989.826 Da / Num. of mol.: 2 / Mutation: A17M, C18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: FA 1090 / Gene: NGO0994 / Plasmid: pET25B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5F809
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5M ammonium sulfate, 15% glycerol, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 10, 2007
RadiationMonochromator: Si (111) double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25438 / % possible obs: 96.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 1.54 / % possible all: 92.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AG0

1ag0


Resolution: 1.9→31.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.042 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22548 1257 5.1 %RANDOM
Rwork0.19091 ---
obs0.19267 23363 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.175 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 24 161 2049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222103
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9732875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.55627.04588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51115379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.41152
X-RAY DIFFRACTIONr_chiral_restr0.0810.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211604
X-RAY DIFFRACTIONr_mcbond_it0.5151.51355
X-RAY DIFFRACTIONr_mcangle_it0.96222201
X-RAY DIFFRACTIONr_scbond_it1.523748
X-RAY DIFFRACTIONr_scangle_it2.574.5661
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 98 -
Rwork0.255 1637 -
obs--92.53 %

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