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- PDB-1vjq: Designed protein based on backbone conformation of procarboxypept... -

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Basic information

Entry
Database: PDB / ID: 1vjq
TitleDesigned protein based on backbone conformation of procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability.
Componentsdesigned proteinDesign
KeywordsSTRUCTURAL GENOMICS / DE NOVO PROTEIN / ENGINEERED PROTEIN / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homologyMetallocarboxypeptidase-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.098 Å
AuthorsMerritt, E.A. / Baker, D. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
Citation
Journal: To be Published
Title: Designed protein based on backbone conformation of procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability.
Authors: Kuhlman, B. / Dantas, G. / Merritt, E.A. / Baker, D.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.
Authors: Dantas, G. / Kuhlman, B. / Callender, D. / Wong, M. / Baker, D.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE DESIGNED PROTEIN BASED ON PROCARBOXYPEPTIDASE-A BACKBONE (1AYE) WITH SIDECHAINS CHOSEN FOR ...SEQUENCE DESIGNED PROTEIN BASED ON PROCARBOXYPEPTIDASE-A BACKBONE (1AYE) WITH SIDECHAINS CHOSEN FOR MAXIMAL PREDICTED STABILITY. DESIGNED SEQUENCE TERMINATES AT GLU 70. RESIDUES 71-79 REMAIN AFTER CLEAVAGE FROM ORIGINAL FUSION PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: designed protein
B: designed protein


Theoretical massNumber of molelcules
Total (without water)18,2882
Polymers18,2882
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.442, 65.041, 39.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein designed protein / Design


Mass: 9144.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Description: Cloned as fusion with structural genomics target Lmaj000047AAA
Plasmid details: Designed protein Cloned as fusion with structural genomics target Lmaj000047AAA
Plasmid: pET3a / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1 ul protein 6.87 mg/ml 1 ul crystallization buffer 20% PEG 1000, 40 mM CaCl, 100 mM NaAc 1 ul micro-seeds of sulfur-Met protein in crystallization buffer, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97954
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 7, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.098→44.721 Å / Num. obs: 8236 / % possible obs: 85 % / Limit h max: 29 / Limit h min: 0 / Limit k max: 30 / Limit k min: 0 / Limit l max: 18 / Limit l min: 0 / Rmerge(I) obs: 0.108
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsDiffraction-ID
2.1-2.1832.90.3751
2.18-2.2653.30.3931
2.26-2.3771.90.3621
2.37-2.4989.10.341
2.49-2.6599.60.3011
2.65-2.851000.2551
2.85-3.141000.171
3.14-3.591000.1021
3.59-4.521000.0711
4.52-501000.0661

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.3 Å / D res low: 50 Å / FOM : 0.48 / Reflection: 7069
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1110.97958.2-7.1
1120.97973-12.4
1130.97875.2-5.2
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
135.28517.7913.209SE32.40.55
236.35716.066.552SE36.60.54
326.13423.1120.222SE600.71
425.92414.1994.814SE52.10.51
Phasing MAD shell
Resolution (Å)FOM Reflection
8.33-500.78391
5.24-8.330.79642
4.09-5.240.74806
3.47-4.090.66930
3.06-3.470.531049
2.77-3.060.361146
2.55-2.770.251174
2.37-2.550.12931
Phasing dmFOM : 0.69 / FOM acentric: 0.7 / FOM centric: 0.68 / Reflection: 7070 / Reflection acentric: 5858 / Reflection centric: 1212
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-44.8530.960.960.88370217153
4.1-6.60.920.940.861035788247
3.3-4.10.870.890.7812731033240
2.9-3.30.760.770.712731074199
2.5-2.90.540.560.4521471866281
2.3-2.50.390.40.3497288092

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
SHELXphasing
RESOLVE2.06phasing
REFMACrefinement
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.098→44.721 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.88 / SU B: 12.164 / SU ML: 0.164 / SU R Cruickshank DPI: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.306 / ESU R Free: 0.265 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2906 386 4.779 %
Rwork0.1991 --
all0.203 --
obs-8077 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 27.261 Å2
Baniso -1Baniso -2Baniso -3
1--1.098 Å20 Å20 Å2
2--3.071 Å20 Å2
3----1.973 Å2
Refinement stepCycle: LAST / Resolution: 2.098→44.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 0 66 1228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221211
X-RAY DIFFRACTIONr_bond_other_d0.0010.021094
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9541657
X-RAY DIFFRACTIONr_angle_other_deg0.8932577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9025144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.04527.19357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.78915202
X-RAY DIFFRACTIONr_chiral_restr0.0980.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02208
X-RAY DIFFRACTIONr_nbd_refined0.1950.2238
X-RAY DIFFRACTIONr_nbd_other0.1840.21085
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2602
X-RAY DIFFRACTIONr_nbtor_other0.0910.2671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4150.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.23
X-RAY DIFFRACTIONr_mcbond_it1.8573888
X-RAY DIFFRACTIONr_mcbond_other0.4083290
X-RAY DIFFRACTIONr_mcangle_it2.38141219
X-RAY DIFFRACTIONr_mcangle_other1.494999
X-RAY DIFFRACTIONr_scbond_it1.0872542
X-RAY DIFFRACTIONr_scbond_other0.21921010
X-RAY DIFFRACTIONr_scangle_it1.733438
X-RAY DIFFRACTIONr_scangle_other0.7831578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.098-2.15210.1780.238172674
2.152-2.2110.344130.232268688
2.211-2.27490.312210.185345658
2.275-2.34470.353260.212390637
2.345-2.42140.317300.219480623
2.421-2.50610.23180.199550615
2.506-2.60040.37320.204553587
2.6-2.70620.381340.211528563
2.706-2.82610.422230.216528551
2.826-2.96340.342270.207487514
2.963-3.1230.253220.203464486
3.123-3.31140.285240.202470494
3.311-3.53870.255190.196414433
3.539-3.82020.27150.171410425
3.82-4.18180.238170.18363380
4.182-4.67020.199170.158348365
4.67-5.3830.237110.167305316
5.383-6.5690.254100.245271281
6.569-9.19130.319120.22208220
9.191-44.72140.38270.283137144
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)
10.48730.36810.67412.3596-2.11344.2372-0.0187-0.01420.05010.07320.00860.11010.08-0.05040.0101-0.0678-0.01120.0266-0.0477-0.0094-0.031234.28416.1833.909
22.07720.61720.38481.78580.48391.39140.00210.0714-0.0144-0.04220.0109-0.0119-0.0510.0386-0.013-0.05240.0234-0.0143-0.04980.0076-0.028827.82214.54214.781
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 73 / Label seq-ID: 1 - 73

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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