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- PDB-3pbj: Hydrolytic catalysis and structural stabilization in a designed m... -

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Basic information

Entry
Database: PDB / ID: 3pbj
TitleHydrolytic catalysis and structural stabilization in a designed metalloprotein
ComponentsCOIL SER L9L-Pen L23H
KeywordsDE NOVO PROTEIN / PARALLEL THREE-STRANDED COILED COIL / MERCURY(II) BINDING PROTEIN / ZINC(II) BINDING PROTEIN / L-PENICILLAMINE
Function / homology:
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZastrow, M.L. / Peacock, A.F.A. / Stuckey, J.A. / Pecoraro, V.L.
CitationJournal: Nat Chem / Year: 2012
Title: Hydrolytic catalysis and structural stabilization in a designed metalloprotein.
Authors: Zastrow, M.L. / Peacock, A.F. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionOct 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 4, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_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: COIL SER L9L-Pen L23H
B: COIL SER L9L-Pen L23H
C: COIL SER L9L-Pen L23H
D: COIL SER L9L-Pen L23H
E: COIL SER L9L-Pen L23H
F: COIL SER L9L-Pen L23H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,26219
Polymers20,2736
Non-polymers98813
Water1,18966
1
A: COIL SER L9L-Pen L23H
B: COIL SER L9L-Pen L23H
C: COIL SER L9L-Pen L23H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5929
Polymers10,1373
Non-polymers4556
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: COIL SER L9L-Pen L23H
E: COIL SER L9L-Pen L23H
F: COIL SER L9L-Pen L23H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,67010
Polymers10,1373
Non-polymers5337
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: COIL SER L9L-Pen L23H
E: COIL SER L9L-Pen L23H
F: COIL SER L9L-Pen L23H
hetero molecules

A: COIL SER L9L-Pen L23H
B: COIL SER L9L-Pen L23H
C: COIL SER L9L-Pen L23H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,26219
Polymers20,2736
Non-polymers98813
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area8400 Å2
ΔGint-298 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.877, 38.649, 75.659
Angle α, β, γ (deg.)90.00, 95.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 6 molecules ABCDEF

#1: Protein/peptide
COIL SER L9L-Pen L23H


Mass: 3378.892 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) artificial gene (others)

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Non-polymers , 5 types, 79 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM NaCl, 28% PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2008 / Details: C(111) CRYSTAL
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 7625 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 40.14 Å2 / Rsym value: 0.058 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.321 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.98 Å / Cor.coef. Fo:Fc: 0.9521 / Cor.coef. Fo:Fc free: 0.9345 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 346 4.54 %RANDOM
Rwork0.2051 ---
obs0.2078 7625 98.54 %-
Displacement parametersBiso mean: 51.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.3269 Å20 Å21.1733 Å2
2--0.4694 Å20 Å2
3----0.1424 Å2
Refine analyzeLuzzati coordinate error obs: 0.388 Å
Refinement stepCycle: LAST / Resolution: 2.2→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1353 0 13 66 1432
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0141375HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.731850HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d657SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes187HARMONIC5
X-RAY DIFFRACTIONt_it1375HARMONIC20
X-RAY DIFFRACTIONt_nbd9SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion3.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1755
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15584
LS refinement shellResolution: 2.2→2.46 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3412 91 4.29 %
Rwork0.2321 2029 -
all0.2369 2120 -
obs--98.54 %
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)
11.57691.1775-1.90361.8932-1.68755.8482-0.0172-0.04880.24420.25960.0209-0.02180.10740.2149-0.0037-0.08720.0224-0.0441-0.0932-0.0340.01926.0293-1.12040.6697
22.365-0.04-3.29651.88021.44456.17540.02460.415-0.1017-0.2418-0.1054-0.0375-0.066-0.50960.0808-0.10690.0404-0.02190.0329-0.0026-0.099716.79450.660137.4903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A,B,C
2X-RAY DIFFRACTION2chain D,E,F

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