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- PDB-4k9j: Structure of Re(CO)3(4,7-dimethyl-phen)(Thr126His)(Lys122Trp)(His... -

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Basic information

Entry
Database: PDB / ID: 4k9j
TitleStructure of Re(CO)3(4,7-dimethyl-phen)(Thr126His)(Lys122Trp)(His83Glu)(Trp48Phe)(Tyr72Phe)(Tyr108Phe)AzCu(II), a Rhenium modified Azurin mutant
ComponentsAzurin
KeywordsELECTRON TRANSPORT / rhenium
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein 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 / Chem-REQ / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTakematsu, K. / Williamson, H.R. / Blanco-Rodriguez, A.M. / Sokolova, L. / Nikolovski, P. / Kaiser, J.T. / Towrie, M. / Clark, I.P. / Vlcek Jr, A. / Winkler, J.R. / Gray, H.B.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Tryptophan-accelerated electron flow across a protein-protein interface.
Authors: Takematsu, K. / Williamson, H. / Blanco-Rodriguez, A.M. / Sokolova, L. / Nikolovski, P. / Kaiser, J.T. / Towrie, M. / Clark, I.P. / Vlcek, A. / Winkler, J.R. / Gray, H.B.
History
DepositionApr 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5173
Polymers13,9751
Non-polymers5422
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.391, 93.215, 109.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

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Components

#1: Protein Azurin /


Mass: 13974.816 Da / Num. of mol.: 1 / Mutation: t126H, k122w, h83e,w48f, y72f
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00282
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-REQ / (1,10 PHENANTHROLINE)-(TRI-CARBON MONOXIDE) RHENIUM (I)


Mass: 478.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12N2O3Re
Details: Synthesis described in: Sullivan, B. P.; Meyer, T. J. J. Chem. Soc., Chem. Commun. 1984, 1244-1245. Connick, W. B.; Di Bilio, A. J.; Schaefer, W. P.; Gray, H. B. Acta Crystallogr. C 1999, C55, 913-916
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: protein buffer:40 mM imidazole, 2 mM NaCl. Reservoir: 100 mM imidazole, 100 mM LiNO3, 6.25 mM CuCl2, 27% PEG 4000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2011 / Details: liquid nitrogen-cooled K-B focusing mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. all: 12166 / Num. obs: 12078 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.099
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-2.035.10.961.8199.8
1.79-1.9199.4
1.7-1.79199.5
1.79-1.9199.4
1.9-2.03199.8
2.03-2.19199.7
2.19-2.4199.7
2.4-2.69199.6
2.69-3.1199.1
3.1-3.8199.7
3.8-5.38198.5
5.38-35198.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4AZU

4azu


Resolution: 1.7→27.346 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 576 4.77 %random
Rwork0.1963 ---
obs0.1982 12064 99.19 %-
all-12166 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→27.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 24 74 1026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015972
X-RAY DIFFRACTIONf_angle_d1.7691324
X-RAY DIFFRACTIONf_dihedral_angle_d15.18324
X-RAY DIFFRACTIONf_chiral_restr0.084148
X-RAY DIFFRACTIONf_plane_restr0.008169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.8710.34591370.28942809X-RAY DIFFRACTION99
1.871-2.14170.26161480.21882853X-RAY DIFFRACTION99
2.1417-2.69790.25681500.212870X-RAY DIFFRACTION100
2.6979-27.34930.20651410.17252956X-RAY DIFFRACTION99
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)
12.78450.6211-1.63985.5181.42.8798-0.2915-0.34080.35320.41460.084-0.3093-0.4215-0.03980.20770.25890.005-0.02590.1212-0.00830.2428-10.5748-8.127522.3753
21.72280.33990.06064.11050.19542.4982-0.2633-0.3248-0.09080.39360.1655-0.2746-0.0930.16490.05720.1992-0.0220.02330.0802-0.01560.2876-7.1021-14.593821.2876
33.368-4.4989-0.89137.744-0.96654.8042-0.08160.80250.5041-0.039-0.08420.4348-0.129-0.56770.24430.1615-0.0239-0.0310.18240.00980.2925-18.695-9.405113.6571
46.1758-1.40721.96275.3051-0.33292.64270.07961.22850.4931-1.06310.0583-0.3385-0.8318-0.22080.08360.4011-0.01590.04770.35760.03770.164-6.6513-8.29184.2414
50.34620.64440.78715.6134-0.37242.546-0.03510.6675-0.5004-0.61720.1710.81480.3064-0.6289-0.00180.258-0.0691-0.15330.6319-0.14430.3584-16.8422-14.53373.9381
62.7595-0.77440.34193.040.21992.5441-0.41871.0087-0.8333-0.39130.09190.36310.4089-0.46040.30050.2152-0.05050.0160.2202-0.0630.3305-11.5955-15.777210.2976
74.0473-4.4394-1.41685.38230.0364.7632-0.45340.5887-0.8207-0.2290.3165-0.10950.4402-0.04520.0920.1897-0.01630.01090.2524-0.11030.3464-3.2055-20.58515.7472
80.2015-1.04450.50755.4604-2.72371.4923-0.34480.69830.30820.4239-0.2863-2.0835-0.47320.85090.53990.3813-0.132-0.0010.4150.01460.84037.619-11.298312.1675
94.5863-0.46280.42853.9216-0.30972.591-0.26820.59670.5864-0.26040.1395-0.4113-0.42540.25410.10510.2235-0.05350.01890.15360.03520.2331-6.1673-5.917313.4615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 48 )
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 66 )
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 75 )
6X-RAY DIFFRACTION6chain 'A' and (resid 76 through 91 )
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 101 )
8X-RAY DIFFRACTION8chain 'A' and (resid 102 through 107 )
9X-RAY DIFFRACTION9chain 'A' and (resid 108 through 128 )

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