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- PDB-3s4t: Crystal structure of putative amidohydrolase-2 (EFI-target 500288... -

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Basic information

Entry
Database: PDB / ID: 3s4t
TitleCrystal structure of putative amidohydrolase-2 (EFI-target 500288)from Polaromonas sp. JS666
ComponentsAmidohydrolase 2
KeywordsHYDROLASE / Enzyme Function Initiative / EFI / Structural Genomics
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
ACETATE ION / Gamma-resorcylate decarboxylase
Similarity search - Component
Biological speciesPolaromonas sp. JS666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRamagopal, U.A. / Toro, R. / Girlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of putative amidohydrolase-2 (EFI-target 500288)from Polaromonas sp. JS666
Authors: Ramagopal, U.A. / Toro, R. / Girlt, J.A. / Almo, S.C.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 13, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidohydrolase 2
B: Amidohydrolase 2
C: Amidohydrolase 2
D: Amidohydrolase 2
E: Amidohydrolase 2
F: Amidohydrolase 2
G: Amidohydrolase 2
H: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,85765
Polymers325,0518
Non-polymers5,80657
Water27,2571513
1
A: Amidohydrolase 2
B: Amidohydrolase 2
C: Amidohydrolase 2
D: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,27732
Polymers162,5254
Non-polymers2,75228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21330 Å2
ΔGint-219 kcal/mol
Surface area43750 Å2
MethodPISA
2
A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,83818
Polymers81,2632
Non-polymers1,57616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-105 kcal/mol
Surface area23500 Å2
MethodPISA
3
C: Amidohydrolase 2
D: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,43914
Polymers81,2632
Non-polymers1,17612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-104 kcal/mol
Surface area22960 Å2
MethodPISA
4
E: Amidohydrolase 2
F: Amidohydrolase 2
G: Amidohydrolase 2
H: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,58033
Polymers162,5254
Non-polymers3,05529
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21700 Å2
ΔGint-231 kcal/mol
Surface area43140 Å2
MethodPISA
5
E: Amidohydrolase 2
F: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,54814
Polymers81,2632
Non-polymers1,28512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-80 kcal/mol
Surface area22740 Å2
MethodPISA
6
G: Amidohydrolase 2
H: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,03219
Polymers81,2632
Non-polymers1,76917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-140 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.024, 151.241, 143.410
Angle α, β, γ (deg.)90.000, 91.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Amidohydrolase 2 /


Mass: 40631.324 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. JS666 (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_2061 / Plasmid: CSH30 L-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q12BV1

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Non-polymers , 6 types, 1570 molecules

#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1513 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris hydrochloride, 2M Ammonium Sulfate, pH 8.5, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 268076 / Num. obs: 268076 / % possible obs: 99.1 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.093 / Χ2: 0.935 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.936.80.59131350.936197.1
1.93-1.976.90.581131490.828197.6
1.97-2.0170.47131580.84197.8
2.01-2.0570.397132380.857198
2.05-2.0970.346132610.87198.3
2.09-2.1470.301133150.888198.6
2.14-2.1970.257133750.907199
2.19-2.256.70.235133591.235199.1
2.25-2.326.80.214133760.975199
2.32-2.397.10.173134220.907199.8
2.39-2.487.10.146134380.92199.4
2.48-2.587.20.129134380.914199.6
2.58-2.77.20.113135210.899199.6
2.7-2.847.20.097134460.92199.7
2.84-3.027.30.084135200.959199.9
3.02-3.257.30.074135311.0441100
3.25-3.587.40.065135631.1331100
3.58-4.096.80.055135111.124199.6
4.09-5.157.20.043135600.8651100
5.15-407.40.037137600.685199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVT

2dvt


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2002 / WRfactor Rwork: 0.1697 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8186 / SU B: 5.916 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1377 / SU Rfree: 0.1276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 12743 5 %RANDOM
Rwork0.1749 ---
obs0.1766 252922 93.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 108.79 Å2 / Biso mean: 24.684 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.05 Å2
2---0.57 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21079 0 338 1513 22930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02222370
X-RAY DIFFRACTIONr_angle_refined_deg1.381.95230422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5752675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29323.3391141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.457153609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.13615194
X-RAY DIFFRACTIONr_chiral_restr0.1010.23126
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117478
X-RAY DIFFRACTIONr_mcbond_it0.71.513295
X-RAY DIFFRACTIONr_mcangle_it1.239221361
X-RAY DIFFRACTIONr_scbond_it2.26839075
X-RAY DIFFRACTIONr_scangle_it3.6014.59061
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 586 -
Rwork0.231 11695 -
all-12281 -
obs--61.13 %
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)
10.5677-0.19810.1690.6923-0.11390.38530.00260.0726-0.0722-0.07770.02660.10390.0336-0.0205-0.02920.0176-0.0162-0.00420.1584-0.01820.04331.768-11.684-13.021
20.7271-0.24060.14480.7678-0.18140.4924-0.0768-0.1078-0.12490.16750.09570.04750.028-0.0529-0.0190.0760.03250.03420.15390.01880.040214.741-21.29416.254
30.7064-0.1334-0.22060.61340.10390.412-0.02350.0790.0408-0.06720.0342-0.0997-0.03060.0027-0.01080.0257-0.019-0.01460.15580.00030.059238.54812.66-12.459
41.0113-0.2936-0.23810.69490.18530.538-0.1062-0.1160.1410.13940.1089-0.0901-0.03380.0315-0.00270.08930.0411-0.06810.1631-0.04030.058725.521.63816.553
50.6073-0.08320.1850.6343-0.06010.3923-0.02720.0572-0.0307-0.07330.0460.0610.0399-0.0158-0.01880.0328-0.01460.00260.01290.00250.099-0.56113.50859.151
60.7163-0.12370.1030.6517-0.16440.4494-0.0501-0.0917-0.10710.11230.0625-0.00290.0516-0.0295-0.01240.08170.0320.0170.02390.02390.105712.364.22587.91
70.5777-0.0927-0.20460.40960.05520.4184-0.02040.06220.0263-0.03970.0345-0.0499-0.03740.021-0.01410.0309-0.0137-0.01510.01660.00020.125136.24738.20359.228
80.7984-0.2122-0.16860.53960.13560.5393-0.0666-0.1080.11470.12760.0777-0.0458-0.05950.0299-0.0110.08520.033-0.04520.0239-0.02460.11823.13147.34688.278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 332
2X-RAY DIFFRACTION2B1 - 324
3X-RAY DIFFRACTION3C1 - 326
4X-RAY DIFFRACTION3D400
5X-RAY DIFFRACTION4D1 - 324
6X-RAY DIFFRACTION5E1 - 325
7X-RAY DIFFRACTION5F400
8X-RAY DIFFRACTION6F1 - 324
9X-RAY DIFFRACTION7G1 - 327
10X-RAY DIFFRACTION8H1 - 324
11X-RAY DIFFRACTION8G349

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