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- PDB-3erx: High-resolution structure of Paracoccus pantotrophus pseudoazurin -

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Basic information

Entry
Database: PDB / ID: 3erx
TitleHigh-resolution structure of Paracoccus pantotrophus pseudoazurin
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / pseudoazurin / copper protein / Paracoccus / high-resolution / Metal-binding / Transport
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 speciesParacoccus pantotrophus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsNajmudin, S. / Pauleta, S.R. / Moura, I. / Romao, M.J.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The 1.4 A resolution structure of Paracoccus pantotrophus pseudoazurin.
Authors: Najmudin, S. / Pauleta, S.R. / Moura, I. / Romao, M.J.
#1: Journal: Biochemistry / Year: 2004
Title: Paracoccus pantotrophus pseudoazurin is an electron donor to cytochrome c peroxidase
Authors: Pauleta, S.R. / Guerlesquin, F. / Goodhew, C.F. / Devreese, B. / Van Beeumen, J. / Pereira, A.S. / Moura, I. / Pettigrew, G.W.
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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_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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1327
Polymers26,7162
Non-polymers4155
Water8,737485
1
A: Pseudoazurin
B: Pseudoazurin
hetero molecules

A: Pseudoazurin
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,26314
Polymers53,4334
Non-polymers83110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5390 Å2
ΔGint-113 kcal/mol
Surface area20490 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-46 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.823, 56.993, 67.982
Angle α, β, γ (deg.)90.00, 126.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pseudoazurin


Mass: 13358.231 Da / Num. of mol.: 2 / Fragment: UNP residues 23 to 145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus pantotrophus (bacteria) / Strain: LMD 52.44 / Gene: pazS / Plasmid: pGEM-T & pET 21-d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P80401
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.0 M ammonium sulphate and 50 mM potassium phosphate at pH 7.0,, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2006
RadiationMonochromator: toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.25→54.88 Å / Num. all: 73293 / Num. obs: 73293 / % possible obs: 79.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 16.3
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4172 / Rsym value: 0.28 / % possible all: 31.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ADW
Resolution: 1.25→54.88 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.135 / SU ML: 0.028 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.053 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20584 3689 5 %RANDOM
Rwork0.18832 ---
all0.1892 73293 --
obs0.1892 69604 79.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.19 Å2
2---0.02 Å20 Å2
3---0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.053 Å0.053 Å
Refinement stepCycle: LAST / Resolution: 1.25→54.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 17 485 2370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222022
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9892749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.26225.85482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.434156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021508
X-RAY DIFFRACTIONr_nbd_refined0.2020.21021
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2392
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.233
X-RAY DIFFRACTIONr_mcbond_it0.5161.51318
X-RAY DIFFRACTIONr_mcangle_it0.81122075
X-RAY DIFFRACTIONr_scbond_it1.3783776
X-RAY DIFFRACTIONr_scangle_it2.1174.5658
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 84 -
Rwork0.32 1685 -
obs-1685 26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.16490.05280.761713.20251.89450.76010.0255-0.0562-0.0536-0.1103-0.02140.20450.00020.0703-0.00410.03480.0027-0.00960.01590.01780.0233-10.753726.989723.8387
21.53620.5057-4.15260.1728-1.319111.5870.0552-0.02160.09260.0707-0.10210.0689-0.3242-0.01020.04690.05410.0126-0.01450.0170.01670.0289-12.432340.467731.1559
31.70780.48430.26890.3480.49060.8573-0.0245-0.01210.0256-0.0131-0.00930.0493-0.07350.02270.03380.0507-0.0079-0.0060.01960.01690.0144-8.01936.952230.6565
41.7834-2.6578-0.64373.98350.97480.243-0.0043-0.1461-0.1931-0.05170.03740.2852-0.04480.0641-0.03310.03580.0105-0.00090.02390.03620.0508-5.896223.021731.093
53.9169-5.94642.327911.8128-6.85446.37160.22140.1582-0.0532-0.0283-0.15660.04210.18230.2464-0.06480.0260.0293-0.0430.00190.00770.0444-5.285517.70422.8557
61.8801-1.496-0.77555.88880.1840.35980.0916-0.0082-0.0705-0.2073-0.07910.0467-0.09770.0491-0.01250.0470.0108-0.02240.02650.00920.0092-10.485731.310620.9102
74.1468-1.9861.0351.8322-0.38020.46930.02470.10780.1573-0.0618-0.0479-0.0547-0.110.13420.02320.0252-0.0087-0.00590.04570.03340.0029-3.910937.121321.195
81.2315-1.638-1.2847.02272.72321.55160.0943-0.0607-0.0495-0.118-0.1447-0.3084-0.0650.1670.0503-0.01680.0168-0.01390.05230.02440.04869.100727.083825.261
99.7306-14.1887.347820.7243-10.90496.53180.41030.39590.2294-0.6124-0.6449-0.42220.34220.36250.23460.01330.04610.01740.05150.03110.00986.935124.228518.641
108.8695-2.7886-0.74881.23410.18830.06950.09410.58260.3494-0.1149-0.14930.037-0.00190.2120.05530.02460.0031-0.00830.10180.0489-0.0021-2.591436.674314.0588
110.6993-0.04650.76074.1770.52550.9071-0.00080.1604-0.03040.01690.06390.0257-0.02810.1503-0.06310.02020.019-0.00840.04220.02150.0154-7.159431.520915.1117
1214.8648-7.95123.87344.2574-2.09791.16670.11820.4082-0.3466-0.0424-0.17880.13490.03940.01580.06060.00140.0435-0.03020.0098-0.01260.08910.406818.209120.6768
131.0298-0.8306-0.08713.6528-0.6040.22870.01750.0624-0.10490.0478-0.00480.0453-0.08940.1671-0.01270.01280.0052-0.01110.04720.01170.0221.904427.939725.9431
141.31750.96520.46241.16980.74230.9781-0.15130.06620.1180.10290.1069-0.0302-0.08730.07410.04440.022-0.0258-0.0230.03980.02250.0316-0.315339.755127.2082
152.14750.2158-0.69359.61611.69630.549-0.0984-0.1978-0.18540.05430.0622-0.0568-0.0550.07550.03620.01190.02340.00070.02450.03910.0527-0.458519.412130.508
165.4145-1.47330.282813.1337-0.03791.3537-0.1193-0.3591-0.22910.19180.40090.0570.25780.25-0.28160.0090.081-0.04070.05650.00870.02278.07919.361233.4455
174.1565-5.95474.105312.8765-4.65634.4-0.09350.13010.06640.33960.1342-0.6865-0.05320.151-0.0407-0.03520.0171-0.0330.0758-0.02170.038510.193429.160134.8295
188.9097-1.5604-0.59072.6329-1.3581.7545-0.1119-0.23770.13650.07010.11270.0378-0.20370.1451-0.00080.0241-0.0382-0.01940.0427-0.00850.00473.856839.644534.2765
191.921-0.8855-0.04232.7129-1.88962.1426-0.1019-0.1925-0.01820.20590.1285-0.0686-0.12410.1512-0.02660.0259-0.0041-0.02370.0606-0.00050.00412.157834.300636.5162
201.85270.82410.1462.01921.53261.31490.0088-0.1745-0.11840.0547-0.0541-0.06330.03360.04870.04530.02510.0203-0.00820.04120.04010.0218-1.368624.364537.5231
210.3179-0.93750.05282.934-0.020.11740.0398-0.0526-0.0115-0.1102-0.0232-0.0054-0.0137-0.053-0.01670.0521-0.0154-0.02550.02020.00190.0251-21.204829.485438.3191
223.4288-0.7918-3.27390.9646-0.44464.96990.13940.0653-0.0774-0.20270.059-0.04010.25790.0209-0.19840.0725-0.01490.0161-0.0103-0.00780.0359-11.90119.361635.4288
231.6291.02240.82172.2822-0.85511.5599-0.03760-0.0171-0.08650.0668-0.03070.0186-0.0116-0.02920.0467-0.0107-0.0080.01330.00770.0192-15.277625.078940.2436
240.5217-1.4123-0.78274.39121.12582.911-0.01420.025-0.0359-0.0949-0.0924-0.0088-0.20540.09220.10660.0606-0.0224-0.02290.0127-0.00850.0113-14.675939.933442.2358
253.375.64471.862712.82381.77631.56550.0136-0.22240.09470.0552-0.07810.0977-0.0604-0.17570.06450.0478-0.0064-0.00860.0243-0.03320.0028-23.632239.448743.5113
260.79750.79061.85193.9762.37044.3899-0.0769-0.041-0.0233-0.150.08220.1341-0.11510.0687-0.00530.0221-0.0373-0.0160.02450.00930.0291-24.185724.547539.4287
271.16110.93521.81732.39061.79652.91190.0893-0.2005-0.12120.0272-0.02140.07740.0826-0.2035-0.06790.0379-0.0443-0.01250.04410.03080.0084-22.352822.223347.1524
280.2109-1.6003-0.400112.71931.87483.10870.1902-0.2749-0.04820.3812-0.23790.327-0.01290.03510.04780.0596-0.0435-0.01190.0703-0.0088-0.0351-15.432832.881657.4064
297.279510.256.049720.32199.90885.3560.1655-0.36510.30320.4228-0.46350.62820.0906-0.32370.2980.0572-0.04370.01850.0528-0.034-0.0278-21.777235.65957.156
308.99215.865510.00716.4929.809915.56170.3257-0.5239-0.14630.1801-0.31360.26860.4239-0.5464-0.01210.0199-0.07110.00540.06590.0194-0.0119-27.687521.915449.2244
312.3335-0.63880.94947.38423.2952.13920.0649-0.3049-0.03220.214-0.03160.15120.0156-0.2319-0.03330.0357-0.0580.00220.05980.002-0.0092-29.307827.855645.5123
324.02583.83144.95914.17835.20996.5606-0.0394-0.14680.0388-0.1503-0.0729-0.0055-0.1843-0.26250.11230.0652-0.0009-0.0150.0231-0.0292-0.0133-22.015941.120450.2004
330.35320.15790.38933.79390.11880.430.0264-0.1872-0.0203-0.018-0.06660.0427-0.03410.01360.04020.0565-0.016-0.00450.0352-0.00480-15.721233.186650.673
341.7874-1.5794-0.69531.61031.20441.89240.2533-0.0873-0.21890.2162-0.09530.02990.2149-0.0702-0.15810.0856-0.0389-0.04720.01050.04450.0332-15.542118.518948.9723
350.28990.93050.29866.21670.70230.379-0.0292-0.0853-0.03760.04180.0556-0.0544-0.0454-0.0183-0.02640.0634-0.0118-0.00860.0223-0.00010.0018-13.900132.937646.2848
363.4832-1.91082.59691.8941-0.15128.9419-0.0434-0.02560.1375-0.02020.3276-0.1296-0.36040.5526-0.28420.0468-0.0561-0.0090.0377-0.0710.0091-9.844343.608151.1972
373.1795-6.29842.713316.0871-3.31014.7585-0.0041-0.09580.16210.25280.1299-0.4205-0.04870.2114-0.12590.0098-0.0106-0.03060.0276-0.02370.0214-4.530134.830554.6052
380.1983-1.5057-0.499813.35356.91656.33590.0207-0.08950.04980.22340.1757-0.24550.14990.3297-0.19640.04910.0058-0.02370.04920.0219-0.0003-6.101122.360954.4708
392.08350.6301-0.06460.1909-0.04622.48190.0246-0.0536-0.05950.0075-0.0109-0.18990.14410.0553-0.01360.05680.0044-0.01690.02210.01220.0073-6.084623.955747.4416
401.2059-0.77440.27444.3053-0.88932.0859-0.01280.03590.07650.1044-0.0422-0.1399-0.00670.14890.05510.0376-0.0309-0.01260.02490.0030.009-6.335.542643.6111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 12
3X-RAY DIFFRACTION3A13 - 19
4X-RAY DIFFRACTION4A20 - 25
5X-RAY DIFFRACTION5A26 - 31
6X-RAY DIFFRACTION6A32 - 36
7X-RAY DIFFRACTION7A37 - 45
8X-RAY DIFFRACTION8A46 - 50
9X-RAY DIFFRACTION9A51 - 56
10X-RAY DIFFRACTION10A57 - 60
11X-RAY DIFFRACTION11A61 - 65
12X-RAY DIFFRACTION12A66 - 71
13X-RAY DIFFRACTION13A72 - 78
14X-RAY DIFFRACTION14A79 - 88
15X-RAY DIFFRACTION15A89 - 94
16X-RAY DIFFRACTION16A95 - 100
17X-RAY DIFFRACTION17A101 - 106
18X-RAY DIFFRACTION18A107 - 111
19X-RAY DIFFRACTION19A112 - 116
20X-RAY DIFFRACTION20A117 - 123
21X-RAY DIFFRACTION21B1 - 9
22X-RAY DIFFRACTION22B10 - 15
23X-RAY DIFFRACTION23B16 - 21
24X-RAY DIFFRACTION24B22 - 26
25X-RAY DIFFRACTION25B27 - 32
26X-RAY DIFFRACTION26B33 - 37
27X-RAY DIFFRACTION27B38 - 45
28X-RAY DIFFRACTION28B46 - 50
29X-RAY DIFFRACTION29B51 - 56
30X-RAY DIFFRACTION30B57 - 61
31X-RAY DIFFRACTION31B62 - 65
32X-RAY DIFFRACTION32B66 - 71
33X-RAY DIFFRACTION33B72 - 77
34X-RAY DIFFRACTION34B78 - 85
35X-RAY DIFFRACTION35B86 - 92
36X-RAY DIFFRACTION36B93 - 98
37X-RAY DIFFRACTION37B99 - 104
38X-RAY DIFFRACTION38B105 - 109
39X-RAY DIFFRACTION39B110 - 116
40X-RAY DIFFRACTION40B117 - 123

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