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- PDB-3mpu: Crystal structure of the C47A/A241C disulfide-linked E. coli Aspa... -

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Basic information

Entry
Database: PDB / ID: 3mpu
TitleCrystal structure of the C47A/A241C disulfide-linked E. coli Aspartate Transcarbamoylase holoenzyme
Components
  • Aspartate carbamoyltransferase catalytic chain
  • Aspartate carbamoyltransferase regulatory chain
KeywordsTRANSFERASE / aspartate trancarbamoylase / disulfide bond / phosphate / catalysis / product release / ordered-sequential mechanism
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / 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 / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.855 Å
AuthorsMendes, K.R. / Kantrowitz, E.R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The Pathway of Product Release from the R State of Aspartate Transcarbamoylase.
Authors: Mendes, K.R. / Kantrowitz, E.R.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase catalytic chain
F: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,20815
Polymers154,4426
Non-polymers7669
Water13,223734
1
A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,41630
Polymers308,88412
Non-polymers1,53218
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area31200 Å2
ΔGint-180 kcal/mol
Surface area99310 Å2
MethodPISA
2
E: Aspartate carbamoyltransferase catalytic chain
F: Aspartate carbamoyltransferase regulatory chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)310,41630
Polymers308,88412
Non-polymers1,53218
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area31760 Å2
ΔGint-180 kcal/mol
Surface area100110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.711, 120.711, 692.471
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21C-476-

HOH

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Components

#1: Protein Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase


Mass: 34337.105 Da / Num. of mol.: 3 / Mutation: C47A, A241C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4245, JW4204, pyrB, pyrI / Plasmid: pEK613 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: pyrI, b4244, JW4203 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7F3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 5.9
Details: Protein at 10 mg/ml was dialyzed against solution containing 100 mM KH2PO4, 3mM NaN3, pH 5.9, MICRODIALYSIS, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2009 / Details: fiber-optic taper
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 45620 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 63.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 10
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 99.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.8 / Num. unique all: 633869 / Rsym value: 0.51 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D09, chain A

1d09


Resolution: 2.855→29.923 Å / SU ML: 1.43 / σ(F): 1.33 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 2302 5.05 %random
Rwork0.1733 ---
obs0.1767 45616 99.18 %-
all-45993 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.943 Å2 / ksol: 0.251 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.4673 Å20 Å20 Å2
2---4.4673 Å20 Å2
3---8.9346 Å2
Refine analyzeLuzzati coordinate error obs: 0.289 Å
Refinement stepCycle: LAST / Resolution: 2.855→29.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10596 0 33 734 11363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710810
X-RAY DIFFRACTIONf_angle_d1.02514661
X-RAY DIFFRACTIONf_dihedral_angle_d17.8933972
X-RAY DIFFRACTIONf_chiral_restr0.0681704
X-RAY DIFFRACTIONf_plane_restr0.0041902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.8555-2.91750.30461480.212450449192
2.9175-2.98530.30251360.21327214525100
2.9853-3.05990.30371430.207126534513100
3.0599-3.14260.31091380.20042701100
3.1426-3.23490.28641520.196826794507100
3.2349-3.33920.27721330.19212701100
3.3392-3.45840.26211460.188627074549100
3.4584-3.59670.27711580.173526844547100
3.5967-3.76010.19861400.16722700100
3.7601-3.95790.23941280.155427254551100
3.9579-4.20520.22111360.150927164581100
4.2052-4.52890.19611430.13822727100
4.5289-4.98280.18361500.133827414650100
4.9828-5.69950.22151520.1623272699
5.6995-7.16440.27541590.1861274899
7.1644-29.92470.20551400.16922935482899

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