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- PDB-1a4c: AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 3.5 CRYSTAL FORM, ... -

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Basic information

Entry
Database: PDB / ID: 1a4c
TitleAZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 3.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / CUPROPROTEIN
Function / homology
Function and homology information


periplasmic space / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / NITRATE ION / Azurin
Similarity search - Component
Biological speciesAchromobacter denitrificans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMesserschmidt, A. / Prade, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH.
Authors: Messerschmidt, A. / Prade, L. / Kroes, S.J. / Sanders-Loehr, J. / Huber, R. / Canters, G.W.
History
DepositionJan 28, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AZURIN
B: AZURIN
C: AZURIN
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,78214
Polymers56,0194
Non-polymers76210
Water8,179454
1
A: AZURIN
C: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3917
Polymers28,0102
Non-polymers3815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AZURIN
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3917
Polymers28,0102
Non-polymers3815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.600, 100.010, 53.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
AZURIN


Mass: 14004.870 Da / Num. of mol.: 4 / Mutation: M121H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter denitrificans (bacteria) / Cellular location: PERIPLASM / Gene: AZU / Plasmid: PCH11 / Gene (production host): AZU / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P00280
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.5 mg/mlprotein1drop
22.0 Mammonium sulfate1drop
30.5 M1dropLiNO3
40.1 Macetate1drop
52.5 Mammonium sulfate1reservoir
60.7 M1reservoirLiNO3
70.14 Macetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: NO MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→27.74 Å / Num. obs: 21288 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.091 / Rsym value: 0.095 / Net I/σ(I): 5.8
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.402 / % possible all: 93.4
Reflection
*PLUS
Highest resolution: 2.45 Å / Num. obs: 19093 / % possible obs: 95.3 % / Redundancy: 3.1 % / Num. measured all: 59933 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
X-PLOR3.8model building
X-PLOR3.8refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AZA

2aza


Resolution: 2.45→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.2093 --
obs0.2093 18540 94.1 %
Displacement parametersBiso mean: 24.09 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 32 454 4398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.45→2.54 Å / Rfactor Rwork: 0.3559 / Total num. of bins used: 8
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
LS refinement shell
*PLUS
Num. reflection obs: 2116

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