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- PDB-5h8j: Crystal structure of Medicago truncatula N-carbamoylputrescine am... -

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Basic information

Entry
Database: PDB / ID: 5h8j
TitleCrystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with cadaverine
ComponentsN-carbamoylputrescine amidohydrolase
KeywordsHYDROLASE / amidase / helical octamer / alpha-beta-beta-alpha sandwich fold / putrescine biosynthesis
Function / homology
Function and homology information


N-carbamoylputrescine amidase / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine
Similarity search - Function
N-carbamoylputrescine amidase / : / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PENTANE-1,5-DIAMINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N-carbamoylputrescine amidase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsSekula, B. / Ruszkowski, M. / Malinska, M. / Dauter, Z.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2014/12/T/ST5/00136 Poland
CitationJournal: Front Plant Sci / Year: 2016
Title: Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants.
Authors: Sekula, B. / Ruszkowski, M. / Malinska, M. / Dauter, Z.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-carbamoylputrescine amidohydrolase
B: N-carbamoylputrescine amidohydrolase
C: N-carbamoylputrescine amidohydrolase
D: N-carbamoylputrescine amidohydrolase
E: N-carbamoylputrescine amidohydrolase
F: N-carbamoylputrescine amidohydrolase
G: N-carbamoylputrescine amidohydrolase
H: N-carbamoylputrescine amidohydrolase
I: N-carbamoylputrescine amidohydrolase
J: N-carbamoylputrescine amidohydrolase
K: N-carbamoylputrescine amidohydrolase
L: N-carbamoylputrescine amidohydrolase
M: N-carbamoylputrescine amidohydrolase
N: N-carbamoylputrescine amidohydrolase
O: N-carbamoylputrescine amidohydrolase
P: N-carbamoylputrescine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)550,64666
Polymers546,09116
Non-polymers4,55650
Water58,4053242
1
A: N-carbamoylputrescine amidohydrolase
B: N-carbamoylputrescine amidohydrolase
C: N-carbamoylputrescine amidohydrolase
D: N-carbamoylputrescine amidohydrolase
E: N-carbamoylputrescine amidohydrolase
F: N-carbamoylputrescine amidohydrolase
G: N-carbamoylputrescine amidohydrolase
H: N-carbamoylputrescine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,55835
Polymers273,0458
Non-polymers2,51327
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40480 Å2
ΔGint-114 kcal/mol
Surface area73490 Å2
MethodPISA
2
I: N-carbamoylputrescine amidohydrolase
J: N-carbamoylputrescine amidohydrolase
K: N-carbamoylputrescine amidohydrolase
L: N-carbamoylputrescine amidohydrolase
M: N-carbamoylputrescine amidohydrolase
N: N-carbamoylputrescine amidohydrolase
O: N-carbamoylputrescine amidohydrolase
P: N-carbamoylputrescine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,08831
Polymers273,0458
Non-polymers2,04323
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39990 Å2
ΔGint-115 kcal/mol
Surface area73460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.269, 211.041, 208.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsOctamers according to Gel filtration

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Components

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
N-carbamoylputrescine amidohydrolase


Mass: 34130.660 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_2g086600 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 GOLD (DE3) / References: UniProt: G7ITU5

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Non-polymers , 6 types, 3292 molecules

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


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-N2P / PENTANE-1,5-DIAMINE


Mass: 102.178 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H14N2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3242 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG3350, 8% Tacsimate at pH 7.0, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 23, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→40 Å / Num. obs: 340107 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.16 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.1
Reflection shellResolution: 2.19→2.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.93 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEdata scaling
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERZ

1erz


Resolution: 2.19→39.56 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.575 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.184 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3402 1 %RANDOM
Rwork0.171 ---
obs0.172 336704 99.09 %-
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: 52.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2---0.65 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.19→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37395 0 301 3242 40938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01938614
X-RAY DIFFRACTIONr_bond_other_d0.0020.0236842
X-RAY DIFFRACTIONr_angle_refined_deg1.61.952143
X-RAY DIFFRACTIONr_angle_other_deg0.9113.01384674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.354717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38124.0771879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.447156480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.25615240
X-RAY DIFFRACTIONr_chiral_restr0.1140.25600
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02143866
X-RAY DIFFRACTIONr_gen_planes_other0.0160.029184
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_it0.731.42818853
X-RAY DIFFRACTIONr_mcbond_other0.731.42818852
X-RAY DIFFRACTIONr_mcangle_it1.2662.13423533
X-RAY DIFFRACTIONr_mcangle_other1.2662.13423534
X-RAY DIFFRACTIONr_scbond_it0.9431.56119761
X-RAY DIFFRACTIONr_scbond_other0.9431.56119761
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4992.27828597
X-RAY DIFFRACTIONr_long_range_B_refined8.70113.30145315
X-RAY DIFFRACTIONr_long_range_B_other8.713.30345316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.25 Å
RfactorNum. reflection% reflection
Rfree0.292 226 -
Rwork0.288 22344 -
obs--89.8 %
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)
11.6274-0.0254-0.31263.02551.64392.2526-0.0523-0.53510.12730.49240.0103-0.0381-0.0763-0.00230.0420.37240.0263-0.00130.5326-0.20330.281538.57292.509-13.363
22.24940.06950.02641.49470.37361.1697-0.0421-0.30190.1313-0.00220.0572-0.2814-0.03180.1601-0.01510.2386-0.00480.03030.3522-0.0710.135657.74274.729-34.307
30.81260.1706-0.0292.25030.15331.2477-0.0405-0.01930.2506-0.3218-0.01510.3304-0.2031-0.09370.05560.32610.0636-0.08480.2801-0.02550.120923.75174.112-54.021
41.00540.16060.09141.75560.28551.07450.02510.1108-0.1008-0.30620.0088-0.08450.05490.0424-0.03390.34130.0573-0.00520.2963-0.02190.013935.85843.804-61.202
51.46570.00270.3791.4446-0.15761.36160.0679-0.2557-0.07970.1117-0.08970.29150.0668-0.20650.02170.2488-0.0450.00150.3932-0.00690.118210.86535.071-32.566
61.5792-0.09890.21121.955-1.00011.44140.1532-0.2734-0.44580.0507-0.1898-0.15560.31640.13050.03660.3994-0.0171-0.07980.38280.1380.28335.2313.18-26.004
71.4967-0.19350.08051.6537-0.0262.13430.086-0.50310.12650.5214-0.1669-0.2566-0.43460.22580.08090.8287-0.2671-0.16840.9271-0.05350.215743.56340.816-0.048
83.1517-0.6960.51931.66370.28741.82380.0869-0.22420.06970.0974-0.068-0.9562-0.09110.7954-0.01890.6203-0.1681-0.26551.25270.06730.877873.83728.947-8.452
91.7541-0.0982-0.53732.99522.13432.5087-0.0214-0.30740.06520.38930.0568-0.0081-0.04070.0926-0.03530.3459-0.04410.05370.369-0.08870.207538.68388.26290.614
102.08950.168-0.28031.38350.31471.1351-0.03-0.18270.1125-0.0170.0684-0.22-0.03510.2326-0.03840.2615-0.06640.06540.3566-0.07250.117458.02970.30870.021
110.95990.2379-0.13342.28730.09531.1842-0.03880.10660.2653-0.35890.0370.3514-0.25-0.05390.00170.37160.0102-0.07050.30520.02480.116523.97769.85450.253
121.0230.32350.03871.73030.07541.0656-0.07830.186-0.1158-0.35940.1-0.08750.02860.0822-0.02160.3459-0.01080.01860.3471-0.04720.016835.74139.38243.293
131.3134-0.26970.54591.4482-0.20511.2283-0.0663-0.1394-0.09050.11080.05440.37950.0314-0.14670.01190.22460.00460.05620.3111-0.0040.162110.3930.96171.801
141.1419-0.25980.33241.4376-0.69731.2580.057-0.0577-0.25020.0846-0.00620.02950.20720.0566-0.05080.32780.03090.01950.29250.0080.166134.5438.9978.631
151.5241-0.31060.07871.18350.21241.9876-0.1511-0.27960.20780.340.0908-0.1379-0.25460.08890.06040.53150.0329-0.08430.5098-0.06450.123142.70336.88104.692
164.03-1.06170.58931.29460.46131.9761-0.09110.00630.27940.17370.1061-0.7091-0.15860.6183-0.01510.4325-0.0002-0.18680.751-0.04690.530273.24825.34396.543
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 303
2X-RAY DIFFRACTION2B1 - 303
3X-RAY DIFFRACTION3C1 - 303
4X-RAY DIFFRACTION4D1 - 303
5X-RAY DIFFRACTION5E1 - 303
6X-RAY DIFFRACTION6F1 - 303
7X-RAY DIFFRACTION7G1 - 303
8X-RAY DIFFRACTION8H1 - 303
9X-RAY DIFFRACTION9I1 - 303
10X-RAY DIFFRACTION10J1 - 303
11X-RAY DIFFRACTION11K1 - 303
12X-RAY DIFFRACTION12L1 - 303
13X-RAY DIFFRACTION13M1 - 303
14X-RAY DIFFRACTION14N1 - 303
15X-RAY DIFFRACTION15O1 - 303
16X-RAY DIFFRACTION16P1 - 303

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