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- PDB-4qrn: HIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXY... -

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Basic information

Entry
Database: PDB / ID: 4qrn
TitleHIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE AND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
Components5-Carboxyvanillate Decarboxylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / DECARBOXYLASE / ENZYME FUNCTION INITIATIVE / EFI / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol
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
4-hydroxy-3-methoxy-5-nitrobenzoic acid / ACETATE ION / : / Amidohydrolase 2
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsPatskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal Structure of 5-Carboxyvanillate Decarboxylase from Novosphingobium Aromaticivorans
Authors: Patskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Raushel, F.M. / Almo, S.C.
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionAug 6, 2014ID: 4ING
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_alt_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_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_alt_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_ptnr1_label_alt_id / _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: 5-Carboxyvanillate Decarboxylase
B: 5-Carboxyvanillate Decarboxylase
C: 5-Carboxyvanillate Decarboxylase
D: 5-Carboxyvanillate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,79327
Polymers169,8254
Non-polymers1,96823
Water36,1202005
1
A: 5-Carboxyvanillate Decarboxylase
B: 5-Carboxyvanillate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,92614
Polymers84,9132
Non-polymers1,01312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-106 kcal/mol
Surface area23510 Å2
MethodPISA
2
C: 5-Carboxyvanillate Decarboxylase
D: 5-Carboxyvanillate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,86713
Polymers84,9132
Non-polymers95411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-102 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.723, 60.747, 130.517
Angle α, β, γ (deg.)90.00, 103.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
5-Carboxyvanillate Decarboxylase


Mass: 42456.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / F199 / Gene: Saro_0799 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GA79

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Non-polymers , 6 types, 2028 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-1DF / 4-hydroxy-3-methoxy-5-nitrobenzoic acid


Mass: 213.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7NO6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2005 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growpH: 8.5
Details: 0.085M TRIS-HCL, PH 8.5, 0.17M SODIUM ACETATE, 25% PEG 4000,15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.92
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.068→50 Å / Num. obs: 614492 / % possible obs: 98.9 % / Observed criterion σ(I): -5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 9.8
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / Rsym value: 0.65 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVT

2dvt


Resolution: 1.07→28.14 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 15.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.155 12447 2.03 %
Rwork0.135 --
obs0.136 614348 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.07→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11134 0 112 2005 13251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111948
X-RAY DIFFRACTIONf_angle_d1.46816217
X-RAY DIFFRACTIONf_dihedral_angle_d13.3334594
X-RAY DIFFRACTIONf_chiral_restr0.0841710
X-RAY DIFFRACTIONf_plane_restr0.012135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0684-1.08060.26013910.255119464X-RAY DIFFRACTION96
1.0806-1.09330.2293940.224520196X-RAY DIFFRACTION100
1.0933-1.10660.21814130.202220245X-RAY DIFFRACTION100
1.1066-1.12060.19144090.191320172X-RAY DIFFRACTION100
1.1206-1.13540.21154240.176320130X-RAY DIFFRACTION100
1.1354-1.15090.17453860.164620249X-RAY DIFFRACTION100
1.1509-1.16740.18634430.152220218X-RAY DIFFRACTION100
1.1674-1.18480.16044220.145420079X-RAY DIFFRACTION100
1.1848-1.20330.15884260.142920265X-RAY DIFFRACTION100
1.2033-1.2230.16974610.140120095X-RAY DIFFRACTION100
1.223-1.24410.16114230.135420210X-RAY DIFFRACTION100
1.2441-1.26670.14934020.127120192X-RAY DIFFRACTION100
1.2667-1.29110.13323820.125920234X-RAY DIFFRACTION100
1.2911-1.31750.15624320.124720226X-RAY DIFFRACTION100
1.3175-1.34610.16024110.125120210X-RAY DIFFRACTION100
1.3461-1.37740.14724420.118420177X-RAY DIFFRACTION100
1.3774-1.41190.13734170.114720305X-RAY DIFFRACTION100
1.4119-1.450.14993860.114520239X-RAY DIFFRACTION100
1.45-1.49270.13784190.112520207X-RAY DIFFRACTION100
1.4927-1.54090.12874620.106620302X-RAY DIFFRACTION100
1.5409-1.59590.13284170.10620271X-RAY DIFFRACTION100
1.5959-1.65980.13024180.106220253X-RAY DIFFRACTION100
1.6598-1.73540.13883900.114220385X-RAY DIFFRACTION100
1.7354-1.82680.14164100.12320262X-RAY DIFFRACTION100
1.8268-1.94130.1464370.125820339X-RAY DIFFRACTION100
1.9413-2.09110.1354280.121220377X-RAY DIFFRACTION100
2.0911-2.30150.14144040.124520377X-RAY DIFFRACTION100
2.3015-2.63430.15274330.134920427X-RAY DIFFRACTION100
2.6343-3.31810.16544140.145519766X-RAY DIFFRACTION96
3.3181-28.14820.17643510.168116029X-RAY DIFFRACTION77

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