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- PDB-4rh4: Zinc-substituted pseudoazurin solved by S/Zn-SAD phasing -

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Basic information

Entry
Database: PDB / ID: 4rh4
TitleZinc-substituted pseudoazurin solved by S/Zn-SAD phasing
ComponentsPseudoazurin
KeywordsMETAL BINDING PROTEIN / SAD / BETA-SANDWICH / DIVALENT METAL-ION / METALLOPROTEIN
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
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.6 Å
AuthorsGessmann, R. / Petratos, K.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Zinc-substituted pseudoazurin solved by S/Zn-SAD phasing.
Authors: Gessmann, R. / Papadovasilaki, M. / Drougkas, E. / Petratos, K.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 28, 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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6414
Polymers13,3841
Non-polymers2583
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.005, 49.005, 98.083
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 Pseudoazurin / Blue copper protein / Cupredoxin


Mass: 13383.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Plasmid: PAB301 / Production host: Escherichia coli (E. coli) / References: UniProt: P04377
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PROTEIN AT 15 MG/ML, 50MM NA-CITRATE, PH 5.8, 20 MM ZNCL2, 2.8 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54178 Å
DetectorType: CUSTOM-MADE / Detector: AREA DETECTOR / Date: May 27, 2014 / Details: Bruker Photon 100 with Cmos technology.
RadiationMonochromator: Helios multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→21.23 Å / Num. all: 17676 / Num. obs: 17521 / % possible obs: 99.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.3 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSIIdata collection
SHELXDphasing
SHELXEmodel building
REFMAC5.7.0032refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→21.2 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.376 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20735 876 5 %RANDOM
Rwork0.18436 ---
obs0.18549 16645 99.12 %-
all-17521 --
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: 13.952 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 11 125 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191123
X-RAY DIFFRACTIONr_bond_other_d0.0010.021176
X-RAY DIFFRACTIONr_angle_refined_deg1.7112.0081539
X-RAY DIFFRACTIONr_angle_other_deg0.82332773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.28727.14342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.20115247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.373151
X-RAY DIFFRACTIONr_chiral_restr0.0990.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
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_it0.6390.815544
X-RAY DIFFRACTIONr_mcbond_other0.630.811543
X-RAY DIFFRACTIONr_mcangle_it1.0731.214689
X-RAY DIFFRACTIONr_mcangle_other0.9971.237688
X-RAY DIFFRACTIONr_scbond_it0.7370.936579
X-RAY DIFFRACTIONr_scbond_other0.7310.917566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1761.346811
X-RAY DIFFRACTIONr_long_range_B_refined4.17.4091316
X-RAY DIFFRACTIONr_long_range_B_other3.8486.831258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 67 -
Rwork0.248 1110 -
obs--89.64 %
Refinement TLS params.Method: refined / Origin x: 21.7675 Å / Origin y: 8.4257 Å / Origin z: -2.8636 Å
111213212223313233
T0.0189 Å2-0.0089 Å2-0.0126 Å2-0.0234 Å2-0.0029 Å2--0.0219 Å2
L0.5661 °2-0.1438 °20.1273 °2-1.9282 °20.1288 °2--0.7322 °2
S-0.0038 Å °-0.0368 Å °0.0008 Å °-0.0148 Å °0.0089 Å °-0.0737 Å °-0.0403 Å °-0.029 Å °-0.0051 Å °

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