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- PDB-4a8t: Crystal structure of putrescine transcarbamylase from Enterococcu... -

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Basic information

Entry
Database: PDB / ID: 4a8t
TitleCrystal structure of putrescine transcarbamylase from Enterococcus faecalis lacking its C-terminal Helix, with bound N5-(phosphonoacetyl) -L-ornithine
ComponentsPUTRESCINE CARBAMOYLTRANSFERASE
KeywordsTRANSFERASE / TRABNSFERASE PALO / DELTA-N-(PHOSPHONOACETYL)-L-ORNITHINE / AGMATINE DEIMINASE ROUTE / AGMATINE CATABOLISM / AGMATINE FERMENTATION / ORNITHINE / ORNITHINE CARBAMOYLTRANSFERASE / ARGININE DEIMINASE / PHOSPHONOACETYLORNITHINE
Function / homology
Function and homology information


putrescine carbamoyltransferase / putrescine biosynthetic process from arginine via N-carbamoylputrescine / putrescine carbamoyltransferase activity / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / amino acid binding / cytoplasm
Similarity search - Function
Putrescine carbamoyltransferase PtcA / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold ...Putrescine carbamoyltransferase PtcA / Ornithine/putrescine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-(PHOSPHONOACETYL)-L-ORNITHINE / TRIETHYLENE GLYCOL / Putrescine carbamoyltransferase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPolo, L.M. / Gil-Ortiz, F. / Rubio, V.
CitationJournal: Plos One / Year: 2012
Title: New Insight Into the Transcarbamylase Family: The Structure of Putrescine Transcarbamylase, a Key Catalyst for Fermentative Utilization of Agmatine
Authors: Polo, L.M. / Gil-Ortiz, F. / Cantin, A. / Rubio, V.
History
DepositionNov 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8404
Polymers38,3771
Non-polymers4633
Water6,972387
1
A: PUTRESCINE CARBAMOYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)233,04224
Polymers230,2646
Non-polymers2,77818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area20550 Å2
ΔGint-46 kcal/mol
Surface area63030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.990, 89.990, 184.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1319-

NI

21A-2036-

HOH

31A-2065-

HOH

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Components

#1: Protein PUTRESCINE CARBAMOYLTRANSFERASE / PTC / PTCASE / AGMATINE CATABOLISM PROTEIN B / PUTRESCINE TRANSCARBAMOYLASE / PUTRESCINE TRANSCARBAMYLASE


Mass: 38377.277 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-317
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN LACKS THE C-TERMINAL HELIX / Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q837U7, putrescine carbamoyltransferase
#2: Chemical ChemComp-PAO / N-(PHOSPHONOACETYL)-L-ORNITHINE


Mass: 254.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15N2O6P
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsY318 WAS REPLACED WITH A STOP CODON, LACKING THE C- TERMINAL HELIX

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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: 3.03 Å3/Da / Density % sol: 59.5 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M MAGNESIUM CHLORIDE, 30% POLYETHYLENE GLYCOL 400, 0.1 M HEPES, PH 7.5, 1 MM N5-(PHOSPHONOACETYL)-L-ORNITHINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.59→40 Å / Num. obs: 60518 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.7
Reflection shellResolution: 1.59→30 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0027refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A8H

4a8h


Resolution: 1.59→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.15 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 76-78 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.18015 3050 5.1 %RANDOM
Rwork0.16218 ---
obs0.16308 57317 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.59→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 27 387 2860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222514
X-RAY DIFFRACTIONr_bond_other_d0.0030.021658
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9673395
X-RAY DIFFRACTIONr_angle_other_deg0.9263.0044046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2735315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58724.912114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66715427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741511
X-RAY DIFFRACTIONr_chiral_restr0.070.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
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_it0.3991.51574
X-RAY DIFFRACTIONr_mcbond_other0.1021.5649
X-RAY DIFFRACTIONr_mcangle_it0.73622522
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4413940
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.34.5873
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.586→1.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 212 -
Rwork0.262 4163 -
obs--99.82 %
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)
11.6444-0.16570.19610.68850.07541.07790.0182-0.0803-0.04960.01530.00490.04120.0012-0.0324-0.0230.01880.00330.00570.00970.01080.016429.461-22.82731.454
20.0005-0.00120.00040.0057-0.00080.00140.010.0052-0.0037-0.0540.00180.01240.00630.0193-0.01170.5428-0.0157-0.04850.3979-0.02630.296435.912-33.3214.252
30.9447-1.07960.27472.1957-0.13540.35160.09070.0936-0.1763-0.1878-0.03970.14950.1087-0.0241-0.05090.0571-0.0199-0.00490.0441-0.01020.050327.607-33.79120.041
40.9473-0.1390.20131.2352-0.37270.96020.01570.02380.0532-0.0954-0.01220.0581-0.0557-0.0392-0.00360.01930.007-0.00110.0123-0.00230.012818.167-10.82719.375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 72
2X-RAY DIFFRACTION2A73 - 82
3X-RAY DIFFRACTION3A83 - 132
4X-RAY DIFFRACTION4A133 - 317

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