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- PDB-4qro: CRYSTAL STRUCTURE of DIHYDROXYBENZOIC ACID DECARBBOXYLASE BPRO_20... -

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Basic information

Entry
Database: PDB / ID: 4qro
TitleCRYSTAL STRUCTURE of DIHYDROXYBENZOIC ACID DECARBBOXYLASE BPRO_2061 (TARGET EFI-500288) FROM POLAROMONAS SP. JS666 WITH BOUND MANGANESE AND AN INHIBITOR, 2-NITRORESORCINOL
ComponentsGamma-resorcylate decarboxylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ENZYME FUNCTION INITIATIVE / EFI / HYDROLASE / DECARBOXYLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


gamma-resorcylate decarboxylase / carboxy-lyase activity / hydrolase activity / metal ion binding
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-nitrobenzene-1,3-diol / ACETATE ION / BICARBONATE ION / : / Gamma-resorcylate decarboxylase
Similarity search - Component
Biological speciesPolaromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPatskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Gerlt, J.A. / Raushel, M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal Structure of Dihydroxybenzoate Decarboxylase from Frompolaromonas Sp WITH BOUND MANGANESE AND 2-NITRORESORCINOL
Authors: Patskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Raushel, F.M. / Almo, S.C.
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / 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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-resorcylate decarboxylase
B: Gamma-resorcylate decarboxylase
C: Gamma-resorcylate decarboxylase
D: Gamma-resorcylate decarboxylase
E: Gamma-resorcylate decarboxylase
F: Gamma-resorcylate decarboxylase
G: Gamma-resorcylate decarboxylase
H: Gamma-resorcylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,61842
Polymers321,6748
Non-polymers2,94334
Water40,3722241
1
A: Gamma-resorcylate decarboxylase
B: Gamma-resorcylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,23311
Polymers80,4192
Non-polymers8149
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-24 kcal/mol
Surface area23350 Å2
MethodPISA
2
C: Gamma-resorcylate decarboxylase
D: Gamma-resorcylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,10810
Polymers80,4192
Non-polymers6898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-24 kcal/mol
Surface area22680 Å2
MethodPISA
3
E: Gamma-resorcylate decarboxylase
F: Gamma-resorcylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,10810
Polymers80,4192
Non-polymers6898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-25 kcal/mol
Surface area22460 Å2
MethodPISA
4
G: Gamma-resorcylate decarboxylase
H: Gamma-resorcylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,16911
Polymers80,4192
Non-polymers7509
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-23 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.958, 151.058, 143.826
Angle α, β, γ (deg.)90.00, 92.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.331923, 0.943304, 0.002411), (0.94329, 0.3319, 0.006811), (0.005625, 0.004535, -0.999974)26.38168, -18.6911, 3.39123
3given(-0.999994, 0.003506, 0.00044), (-0.003508, -0.999986, -0.003965), (0.000427, -0.003966, 0.999992)40.26173, 0.99112, 0.02425
4given(0.328597, -0.94447, 7.6E-5), (-0.944459, -0.328593, 0.004821), (-0.004528, -0.001656, -0.999988)13.89671, 19.58213, 3.55689
5given(0.999999, 0.000337, 0.001608), (-0.000335, 0.999999, -0.001025), (-0.001608, 0.001024, 0.999998)2.50898, -25.07674, -71.85206
6given(-0.332856, 0.942969, 0.004068), (0.942971, 0.332834, 0.005315), (0.003658, 0.005605, -0.999978)1.49106, -24.94596, 75.11611
7given(-0.999998, 0.001851, -0.000873), (-0.001847, -0.999987, -0.004757), (-0.000882, -0.004755, 0.999988)37.64933, 26.38963, -71.70919
8given(0.328619, -0.944462, -0.001221), (-0.944453, -0.328622, 0.004103), (-0.004276, -0.000195, -0.999991)38.63228, 25.05453, 75.4174

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Gamma-resorcylate decarboxylase


Mass: 40209.270 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_2061 / References: UniProt: Q12BV1

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Non-polymers , 6 types, 2275 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-38L / 2-nitrobenzene-1,3-diol


Mass: 155.108 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H5NO4
#6: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2241 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growpH: 4.6
Details: 0.1M SODIUM ACETATE, PH 4.6, 1M AMMONIUM CITRATE DIBASIC, 5MM MANGANESE CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 412849 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 12.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.67 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0071refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S4T

3s4t


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.992 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22344 12420 3 %RANDOM
Rwork0.18917 ---
obs0.1902 399829 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.361 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0 Å20.26 Å2
2---1.99 Å2-0 Å2
3---3.42 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21059 0 180 2241 23480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01922209
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220624
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.94530191
X-RAY DIFFRACTIONr_angle_other_deg0.832.99947281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78952669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33523.3631142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.609153570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.46915193
X-RAY DIFFRACTIONr_chiral_restr0.1240.23138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02125475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025530
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.6686.30110547
X-RAY DIFFRACTIONr_mcbond_other6.6376.29810535
X-RAY DIFFRACTIONr_mcangle_it6.4069.35413188
X-RAY DIFFRACTIONr_mcangle_other6.4089.35513189
X-RAY DIFFRACTIONr_scbond_it14.8287.40211662
X-RAY DIFFRACTIONr_scbond_other14.7617.39911657
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.00310.5216978
X-RAY DIFFRACTIONr_long_range_B_refined12.17523.74427905
X-RAY DIFFRACTIONr_long_range_B_other12.17423.74627906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 839 -
Rwork0.363 29473 -
obs--99.32 %

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