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- PDB-3e59: Crystal structure of the PvcA (PA2254) protein from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 3.0E+59
TitleCrystal structure of the PvcA (PA2254) protein from Pseudomonas aeruginosa
ComponentsPyoverdine biosynthesis protein PvcA
KeywordsTRANSFERASE / PvcA / isonitrile / paerucumarin / 2-isocyano-6 / 7-dihydroxycoumarin
Function / homology
Function and homology information


Wheat Germ Agglutinin (Isolectin 2); domain 1 - #140 / Isocyanide synthase/Spore wall maturation protein DIT1 / L-tyrosine isonitrile synthase / Pyoverdine/dityrosine biosynthesis protein / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / Paerucumarin biosynthesis protein PvcA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsGulick, A.M. / Drake, E.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin.
Authors: Drake, E.J. / Gulick, A.M.
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyoverdine biosynthesis protein PvcA
B: Pyoverdine biosynthesis protein PvcA
C: Pyoverdine biosynthesis protein PvcA
D: Pyoverdine biosynthesis protein PvcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,38512
Polymers149,5154
Non-polymers8708
Water7,512417
1
A: Pyoverdine biosynthesis protein PvcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5693
Polymers37,3791
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyoverdine biosynthesis protein PvcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7744
Polymers37,3791
Non-polymers3953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Pyoverdine biosynthesis protein PvcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4742
Polymers37,3791
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Pyoverdine biosynthesis protein PvcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5693
Polymers37,3791
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.226, 132.530, 96.897
Angle α, β, γ (deg.)90.00, 97.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyoverdine biosynthesis protein PvcA


Mass: 37378.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: pvcA, PA2254 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I1L5
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 41-45% PEG 1000, 35-50 mM KH2PO4, 100 mM TrisHCl, pH 9.0, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11131
21131
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-110.979
SYNCHROTRONSSRL BL9-120.97922, 0.97957, 0.9567
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 23, 2008
ADSC QUANTUM 3152CCDFeb 25, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979221
30.979571
40.95671
ReflectionResolution: 2.1→50 Å / Num. all: 82701 / Num. obs: 77408 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.314 / % possible all: 0.618

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.798 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24618 3546 5 %RANDOM
Rwork0.19699 ---
all0.19955 ---
obs0.19955 67528 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.106 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å20.73 Å2
2---0.53 Å20 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9579 0 50 417 10046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.97213453
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29951238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19422.926458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72151573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.541593
X-RAY DIFFRACTIONr_chiral_restr0.0810.21488
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027621
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.24402
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.26794
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2531
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.79726358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.66839855
X-RAY DIFFRACTIONr_scbond_it2.05624003
X-RAY DIFFRACTIONr_scangle_it3.00833596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 57 -
Rwork0.221 1196 -
obs-1196 57.01 %
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)
10.5042-0.2279-0.01252.6813-0.73251.3836-0.07-0.10550.094-0.00810.2670.12130.0664-0.056-0.1971-0.1014-0.0028-0.0262-0.0666-0.0013-0.0934-5.70913.977-38.276
27.2417-0.5351-2.053610.62830.53369.1726-0.210.2595-0.3247-1.60840.4745-0.17390.52320.1712-0.26450.2391-0.1214-0.0611-0.13080.0275-0.2048-3.332-0.828-56.004
30.7084-0.2305-0.30012.01830.36640.4936-0.0983-0.1024-0.0670.09080.10230.16540.00650.0797-0.004-0.0760.02930.0063-0.0950.0632-0.0641-3.739-27.301-38.444
45.77152.2167-1.73427.2396-1.21082.24020.1189-0.02960.210.7962-0.0911.2153-0.0379-0.1123-0.028-0.12470.02490.1146-0.1550.0520.0845-22.2-13.639-31.463
51.70580.3341-0.25443.2786-0.23620.341-0.1860.0889-0.1174-0.24540.1641-0.16090.0625-0.03630.022-0.053-0.02630.0507-0.1247-0.0269-0.0884-17.0837.566-8.338
66.3579-0.4344-1.76279.7035-2.3083.1052-0.16280.13690.0339-1.20240.1808-2.00790.084-0.0191-0.018-0.083-0.04060.231-0.2315-0.10270.22051.4550.941-14.708
70.77370.0019-0.22732.20210.16551.4510.0044-0.0263-0.0017-0.08820.0511-0.0241-0.03740.0895-0.0556-0.0724-0.04740.0353-0.11860.0161-0.0963-15.71478.468-9.962
84.9445-1.12972.00567.18540.53895.81290.1924-0.2624-0.25010.8028-0.1207-0.16640.1851-0.1994-0.07170.0863-0.0673-0.0278-0.1050.0433-0.1512-18.29364.2288.55
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 26810 - 270
2X-RAY DIFFRACTION2AA280 - 317282 - 319
3X-RAY DIFFRACTION3BB8 - 26810 - 270
4X-RAY DIFFRACTION4BB280 - 318282 - 320
5X-RAY DIFFRACTION5CC8 - 26810 - 270
6X-RAY DIFFRACTION6CC280 - 317282 - 319
7X-RAY DIFFRACTION7DD6 - 2688 - 270
8X-RAY DIFFRACTION8DD280 - 318282 - 320

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