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- PDB-3tp4: Crystal Structure of engineered protein at the resolution 1.98A, ... -

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Basic information

Entry
Database: PDB / ID: 3tp4
TitleCrystal Structure of engineered protein at the resolution 1.98A, Northeast Structural Genomics Consortium Target OR128
Componentscomputational Design of Enzyme
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / OR128 / OSH97
Function / homology
Function and homology information


Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DI(HYDROXYETHYL)ETHER
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Rajagopalan, S. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Baker, D. / Montelione, G.T. ...Kuzin, A. / Su, M. / Seetharaman, J. / Rajagopalan, S. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Baker, D. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Design of activated serine-containing catalytic triads with atomic-level accuracy.
Authors: Rajagopalan, S. / Wang, C. / Yu, K. / Kuzin, A.P. / Richter, F. / Lew, S. / Miklos, A.E. / Matthews, M.L. / Seetharaman, J. / Su, M. / Hunt, J.F. / Cravatt, B.F. / Baker, D.
History
DepositionSep 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Sep 13, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: computational Design of Enzyme
B: computational Design of Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6116
Polymers100,3612
Non-polymers2514
Water13,241735
1
A: computational Design of Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2402
Polymers50,1801
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: computational Design of Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3714
Polymers50,1801
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.666, 113.943, 116.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein computational Design of Enzyme


Mass: 50180.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pet29b / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: NaAcetate - 0.2M, NaCacodylate 0.1M, PEG8K - 30%, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.979→30 Å / Num. obs: 154916 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.7 / % possible all: 95.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BVY

2bvy


Resolution: 1.979→29.256 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.64 / σ(F): 1.33 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 4074 5.01 %
Rwork0.1783 --
obs0.1803 81260 97.91 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.928 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5416 Å2-0 Å2-0 Å2
2---0.2065 Å20 Å2
3----4.3351 Å2
Refinement stepCycle: LAST / Resolution: 1.979→29.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6770 0 16 735 7521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076945
X-RAY DIFFRACTIONf_angle_d1.0059499
X-RAY DIFFRACTIONf_dihedral_angle_d13.1432330
X-RAY DIFFRACTIONf_chiral_restr0.0691068
X-RAY DIFFRACTIONf_plane_restr0.0041256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9792-2.00250.341880.30561780X-RAY DIFFRACTION66
2.0025-2.02690.31131400.25722636X-RAY DIFFRACTION99
2.0269-2.05260.26231640.24032643X-RAY DIFFRACTION100
2.0526-2.07960.25631510.22192654X-RAY DIFFRACTION100
2.0796-2.1080.26721230.21122736X-RAY DIFFRACTION100
2.108-2.13810.26381420.20262661X-RAY DIFFRACTION100
2.1381-2.170.24551410.19922718X-RAY DIFFRACTION100
2.17-2.20390.24591570.19362654X-RAY DIFFRACTION100
2.2039-2.24010.2861180.20222718X-RAY DIFFRACTION100
2.2401-2.27870.25551410.21012683X-RAY DIFFRACTION100
2.2787-2.32010.27361500.20182664X-RAY DIFFRACTION100
2.3201-2.36470.24631400.18882720X-RAY DIFFRACTION100
2.3647-2.41290.22511370.17232684X-RAY DIFFRACTION100
2.4129-2.46540.21571280.18832696X-RAY DIFFRACTION100
2.4654-2.52270.26131500.19322683X-RAY DIFFRACTION100
2.5227-2.58580.22541340.19162717X-RAY DIFFRACTION100
2.5858-2.65560.20811510.18232684X-RAY DIFFRACTION99
2.6556-2.73370.25311530.16982677X-RAY DIFFRACTION99
2.7337-2.82190.21541350.17472695X-RAY DIFFRACTION99
2.8219-2.92270.22481380.18632696X-RAY DIFFRACTION99
2.9227-3.03960.22881470.18852673X-RAY DIFFRACTION99
3.0396-3.17770.2831290.19382730X-RAY DIFFRACTION99
3.1777-3.3450.25781450.19472712X-RAY DIFFRACTION99
3.345-3.55430.19991360.18712701X-RAY DIFFRACTION99
3.5543-3.82820.18851420.17892701X-RAY DIFFRACTION99
3.8282-4.21240.19831320.14382723X-RAY DIFFRACTION98
4.2124-4.81960.13471630.12942679X-RAY DIFFRACTION97
4.8196-6.06330.18641520.14972704X-RAY DIFFRACTION97
6.0633-29.25920.22211470.18342764X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 0.7166 Å / Origin y: -5.9576 Å / Origin z: 2.5477 Å
111213212223313233
T0.1567 Å2-0.009 Å20.0159 Å2-0.143 Å20.0014 Å2--0.1359 Å2
L0.2603 °20.0341 °2-0.0594 °2-0.4673 °20.0877 °2--0.2885 °2
S-0.0089 Å °0.0198 Å °0.0123 Å °-0.0073 Å °0.0049 Å °-0.0575 Å °0.0073 Å °0.001 Å °0.0106 Å °
Refinement TLS groupSelection details: all

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