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- PDB-2phd: Crystal Structure Determination of a Salicylate 1,2-Dioxygenase f... -

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Basic information

Entry
Database: PDB / ID: 2phd
TitleCrystal Structure Determination of a Salicylate 1,2-Dioxygenase from Pseudaminobacter salicylatoxidans
ComponentsGentisate 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / beta-sandwich
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / Gentisate 1,2-dioxygenase
Similarity search - Component
Biological speciesPseudaminobacter salicylatoxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMatera, I. / Ferraroni, M. / Briganti, F.
CitationJournal: To be Published
Title: Crystal Structure Determination of a Salicylate 1,2-Dioxygenase from Pseudaminobacter salicylatoxidans
Authors: Ferraroni, M. / Matera, I. / Briganti, F. / Stolz, A. / Burger, S.
History
DepositionApr 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_comp_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_comp_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gentisate 1,2-dioxygenase
B: Gentisate 1,2-dioxygenase
C: Gentisate 1,2-dioxygenase
D: Gentisate 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,06114
Polymers164,5784
Non-polymers48310
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.016, 133.016, 190.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D
331A
341B
351C
361D
371A
381B
391C
401D
411A
421B
431C
441D
451A
461B
471C
481D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARG2AA46 - 6946 - 69
21METMETARGARG2BB46 - 6946 - 69
31METMETARGARG2CC46 - 6946 - 69
41METMETARGARG2DD46 - 6946 - 69
52LYSLYSGLUGLU6AA70 - 8270 - 82
62LYSLYSGLUGLU6BB70 - 8270 - 82
72LYSLYSGLUGLU6CC70 - 8270 - 82
82LYSLYSGLUGLU6DD70 - 8270 - 82
93ARGARGHISHIS2AA83 - 16283 - 162
103ARGARGHISHIS2BB83 - 16283 - 162
113ARGARGHISHIS2CC83 - 16283 - 162
123ARGARGHISHIS2DD83 - 16283 - 162
134METMETMETMET5AA163163
144METMETMETMET5BB163163
154METMETMETMET5CC163163
164METMETMETMET5DD163163
175ASNASNPHEPHE2AA164 - 191164 - 191
185ASNASNPHEPHE2BB164 - 191164 - 191
195ASNASNPHEPHE2CC164 - 191164 - 191
205ASNASNPHEPHE2DD164 - 191164 - 191
216GLYGLYARGARG6AA192 - 209192 - 209
226GLYGLYARGARG6BB192 - 209192 - 209
236GLYGLYARGARG6CC192 - 209192 - 209
246GLYGLYARGARG6DD192 - 209192 - 209
257LEULEUASNASN2AA210 - 296210 - 296
267LEULEUASNASN2BB210 - 296210 - 296
277LEULEUASNASN2CC210 - 296210 - 296
287LEULEUASNASN2DD210 - 296210 - 296
298GLUGLUSERSER5AA297 - 300297 - 300
308GLUGLUSERSER5BB297 - 300297 - 300
318GLUGLUSERSER5CC297 - 300297 - 300
328GLUGLUSERSER5DD297 - 300297 - 300
339THRTHRLEULEU2AA301 - 321301 - 321
349THRTHRLEULEU2BB301 - 321301 - 321
359THRTHRLEULEU2CC301 - 321301 - 321
369THRTHRLEULEU2DD301 - 321301 - 321
3710GLUGLUGLUGLU5AA322322
3810GLUGLUGLUGLU5BB322322
3910GLUGLUGLUGLU5CC322322
4010GLUGLUGLUGLU5DD322322
4111LYSLYSLYSLYS2AA323 - 363323 - 363
4211LYSLYSLYSLYS2BB323 - 363323 - 363
4311LYSLYSLYSLYS2CC323 - 363323 - 363
4411LYSLYSLYSLYS2DD323 - 363323 - 363
4512ILEILEGLNGLN6AA364 - 367364 - 367
4612ILEILEGLNGLN6BB364 - 367364 - 367
4712ILEILEGLNGLN6CC364 - 367364 - 367
4812ILEILEGLYGLY6DD364 - 366364 - 366

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Components

#1: Protein
Gentisate 1,2-dioxygenase


Mass: 41144.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudaminobacter salicylatoxidans (bacteria)
Strain: BN12 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q67FT0, gentisate 1,2-dioxygenase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 12% w/v EtOH, 4% w/v PEG400, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 28, 2005
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.9→109.109 Å / Num. all: 38103 / Num. obs: 38103 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 4.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.47 / % possible all: 99.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å109.11 Å
Translation3 Å109.11 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D40

2d40


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.864 / SU B: 16.447 / SU ML: 0.31 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26239 1894 5 %RANDOM
Rwork0.19313 ---
obs0.19656 35989 98.46 %-
all-37883 --
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: 42.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.67 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10842 0 16 174 11032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02111159
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.94315201
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44151388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92223.256516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.232151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5481587
X-RAY DIFFRACTIONr_chiral_restr0.1140.21616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028754
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.25551
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.27394
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2452
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1030.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6091.57091
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.079211143
X-RAY DIFFRACTIONr_scbond_it1.434682
X-RAY DIFFRACTIONr_scangle_it2.2574.54058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1124tight positional0.060.05
2B1124tight positional0.070.05
3C1124tight positional0.060.05
4D1124tight positional0.060.05
1A1093medium positional0.40.5
2B1093medium positional0.440.5
3C1093medium positional0.390.5
4D1093medium positional0.430.5
1A207loose positional0.925
2B207loose positional1.265
3C207loose positional0.945
4D207loose positional1.555
1A1124tight thermal0.120.5
2B1124tight thermal0.120.5
3C1124tight thermal0.110.5
4D1124tight thermal0.130.5
1A1093medium thermal0.852
2B1093medium thermal0.942
3C1093medium thermal0.82
4D1093medium thermal0.882
1A207loose thermal4.2810
2B207loose thermal3.1610
3C207loose thermal4.0710
4D207loose thermal3.0310
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 127 -
Rwork0.288 2611 -
obs--99.46 %

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