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- PDB-1zlp: Petal death protein PSR132 with cysteine-linked glutaraldehyde fo... -

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Basic information

Entry
Database: PDB / ID: 1zlp
TitlePetal death protein PSR132 with cysteine-linked glutaraldehyde forming a thiohemiacetal adduct
Componentspetal death protein
KeywordsLYASE / TIM-barrel / helix swapping / 2-ethyl-3-methylmalate lyase / 2-propyl-3-methylmalate lyase / lyase/PEP mutase superfamily
Function / homology
Function and homology information


oxaloacetase / oxaloacetase activity / citramalate lyase activity / Lyases; Carbon-carbon lyases; Oxo-acid-lyases / oxaloacetate metabolic process / transferase activity / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Phosphoenolpyruvate phosphomutase / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-HYDROXYPENTANAL / Petal death protein
Similarity search - Component
Biological speciesDianthus caryophyllus (clove pink)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsTeplyakov, A. / Liu, S. / Lu, Z. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of the Petal Death Protein from Carnation Flower.
Authors: Teplyakov, A. / Liu, S. / Lu, Z. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionMay 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE LIGAND IS A COVALENT ADDUCT (THIOHEMIACETAL) FORMED BETWEEN GLUTARALDEHYDE (AKA 1,5- ...HETEROGEN THE LIGAND IS A COVALENT ADDUCT (THIOHEMIACETAL) FORMED BETWEEN GLUTARALDEHYDE (AKA 1,5-PENTANEDIAL OR 1,5-PENTANEDIONE, OR 5-OXO-PENTANAL) AND THE THIOL GROUP OF CYS144.
Remark 999SEQUENCE THE AUTHORS STATE THAT THE FUNCTIONAL ANNOTATION OF THE SWS ENTRY BASED ON SEQUENCE ...SEQUENCE THE AUTHORS STATE THAT THE FUNCTIONAL ANNOTATION OF THE SWS ENTRY BASED ON SEQUENCE HOMOLOGY AS CARBOXYPEP MUTASE IS WRONG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: petal death protein
B: petal death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6996
Polymers68,4462
Non-polymers2534
Water1,24369
1
A: petal death protein
B: petal death protein
hetero molecules

A: petal death protein
B: petal death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,39712
Polymers136,8924
Non-polymers5068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area21230 Å2
ΔGint-173 kcal/mol
Surface area37010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)156.190, 156.190, 75.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein petal death protein / PSR132


Mass: 34222.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dianthus caryophyllus (clove pink) / Gene: PSR132 / Plasmid: PSR132-pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS
References: UniProt: Q05957, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GAQ / 5-HYDROXYPENTANAL


Mass: 102.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.86 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris, 12% PEG 20K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.2755, 0.9792, 0.9799, 0.9724
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2002 / Details: cylindrically bent Pt-coated mirror
RadiationMonochromator: Si(111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.27551
20.97921
30.97991
40.97241
ReflectionResolution: 2.7→29.5 Å / Num. all: 26327 / Num. obs: 26327 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 41.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→10 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 25.979 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24998 2000 7.8 %RANDOM
Rwork0.19535 ---
obs0.19968 23720 100 %-
all-23720 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 82.746 Å2
Baniso -1Baniso -2Baniso -3
1--10.46 Å2-5.23 Å20 Å2
2---10.46 Å20 Å2
3---15.69 Å2
Refine analyzeLuzzati coordinate error free: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 16 69 4411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214420
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.955959
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40923.946185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.13515763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8781528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2679
X-RAY DIFFRACTIONr_gen_planes_refined00.023286
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2980.22343
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.22988
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.2148
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.40132863
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.35644496
X-RAY DIFFRACTIONr_scbond_it10.13181701
X-RAY DIFFRACTIONr_scangle_it12.77281463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 104 -
Rwork0.341 1178 -
obs--100 %
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)
15.0818-0.53141.41923.81650.29981.19350.08180.3151-0.321-0.3782-0.04440.31330.1506-0.0209-0.0374-0.0632-0.0342-0.0571-0.0942-0.0598-0.5958-48.421758.28844.3327
24.12730.3919-1.24042.2625-0.3341.527-0.05870.581.3368-0.40050.15170.6472-0.2606-0.2023-0.09310.0016-0.0461-0.0861-0.06260.22380.2039-45.127296.71890.7063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA28 - 31128 - 311
2X-RAY DIFFRACTION2BB28 - 31128 - 311

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