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- PDB-1pmy: REFINED CRYSTAL STRUCTURE OF PSEUDOAZURIN FROM METHYLOBACTERIUM E... -

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Basic information

Entry
Database: PDB / ID: 1pmy
TitleREFINED CRYSTAL STRUCTURE OF PSEUDOAZURIN FROM METHYLOBACTERIUM EXTORQUENS AM1 AT 1.5 ANGSTROMS RESOLUTION
ComponentsPSEUDOAZURIN
KeywordsELECTRON TRANSFER(CUPROPROTEIN)
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 ...Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 / Pseudoazurin
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsInoue, T. / Kai, Y. / Harada, S. / Kasai, N. / Ohshiro, Y. / Suzuki, S. / Kohzuma, T. / Tobari, J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined crystal structure of pseudoazurin from Methylobacterium extorquens AM1 at 1.5 A resolution.
Authors: Inoue, T. / Kai, Y. / Harada, S. / Kasai, N. / Ohshiro, Y. / Suzuki, S. / Kohzuma, T. / Tobari, J.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Preliminary Crystallographic Study of a Pseudoazurin from Methylotrophic Bacterium, Methylobacterium Extorquens Am1
Authors: Inoue, T. / Kai, Y. / Harada, S. / Kasai, N. / Suzuki, S. / Kohzuma, T. / Tobari, J.
History
DepositionJan 28, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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

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Assembly

Deposited unit
A: PSEUDOAZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4742
Polymers13,4111
Non-polymers641
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.619, 63.280, 35.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 20

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Components

#1: Protein PSEUDOAZURIN


Mass: 13410.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / References: UniProt: P04171
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMpotassium phosphate1drop
31 mMsodium azide1drop
440 %satammonium sulfate1drop
550 mMpotassium phosphate1reservoir
61 mMsodium azide1reservoir
767 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 15 Å / Num. obs: 25154 / Num. measured all: 94051 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 3 Å / Num. measured obs: 50881 / Rmerge(I) obs: 0.039

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.5→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.199 -
obs0.199 14365
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 1 132 1070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.024
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_deg
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
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.039
X-RAY DIFFRACTIONx_planar_d0.044

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