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- PDB-1zpe: Arginase I covalently modified with butylamine at Q19C -

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Basic information

Entry
Database: PDB / ID: 1zpe
TitleArginase I covalently modified with butylamine at Q19C
ComponentsArginase 1Arginase
KeywordsHYDROLASE / chemically modified enzyme
Function / homology
Function and homology information


regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginine metabolic process / arginine catabolic process to ornithine / response to selenium ion / arginase ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginine metabolic process / arginine catabolic process to ornithine / response to selenium ion / arginase / arginase activity / urea cycle / response to methylmercury / response to vitamin A / response to herbicide / response to steroid hormone / response to manganese ion / Neutrophil degranulation / response to zinc ion / negative regulation of type II interferon-mediated signaling pathway / cellular response to glucagon stimulus / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / maternal process involved in female pregnancy / response to axon injury / response to vitamin E / response to amino acid / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / cellular response to interleukin-4 / positive regulation of endothelial cell proliferation / cellular response to dexamethasone stimulus / liver development / female pregnancy / lung development / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to lipopolysaccharide / adaptive immune response / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ureohydrolase domain / Arginase / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsColleluori, D.M. / Reczkowski, R.S. / Emig, F.A. / Cama, E. / Cox, J.D. / Scolnick, L.R. / Compher, K. / Jude, K. / Han, S. / Viola, R.E. ...Colleluori, D.M. / Reczkowski, R.S. / Emig, F.A. / Cama, E. / Cox, J.D. / Scolnick, L.R. / Compher, K. / Jude, K. / Han, S. / Viola, R.E. / Christianson, D.W. / Ash, D.E.
CitationJournal: Arch.Biochem.Biophys. / Year: 2005
Title: Probing the role of the hyper-reactive histidine residue of arginase.
Authors: Colleluori, D.M. / Reczkowski, R.S. / Emig, F.A. / Cama, E. / Cox, J.D. / Scolnick, L.R. / Compher, K. / Jude, K. / Han, S. / Viola, R.E. / Christianson, D.W. / Ash, D.E.
History
DepositionMay 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginase 1
B: Arginase 1
C: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0839
Polymers101,7533
Non-polymers3306
Water8,773487
1
A: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0283
Polymers33,9181
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0283
Polymers33,9181
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0283
Polymers33,9181
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-62 kcal/mol
Surface area34070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.078, 88.078, 106.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Arginase 1 / Arginase / Liver-type arginase


Mass: 33917.738 Da / Num. of mol.: 3 / Mutation: C119A, C168A, C303A, H141A, Q19(BBC)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arg1 / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07824, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9124 Å / Relative weight: 1
ReflectionResolution: 1.7→28.83 Å / Num. all: 101497 / Num. obs: 100416 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.088
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.299 / Num. unique all: 14712 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RLA

1rla


Resolution: 1.7→28.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1721269.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 5067 5 %RANDOM
Rwork0.206 ---
obs0.206 100416 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4576 Å2 / ksol: 0.393894 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20.72 Å20 Å2
2---0.26 Å20 Å2
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7173 0 6 487 7666
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.622.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 816 5 %
Rwork0.251 15448 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1mm19_protein_rep.parammm19_protein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4cispep2.paramcispep.param

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