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- PDB-6qaf: Crystal structure of human Arginase-1 at pH 9.0 in complex with C... -

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Basic information

Entry
Database: PDB / ID: 6qaf
TitleCrystal structure of human Arginase-1 at pH 9.0 in complex with CB-1158/INCB001158
ComponentsArginase-1
KeywordsHYDROLASE / arignase inhibitor / borate / manganese cluster / pH-dependent
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan ...positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / L-arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Arginase / Ureohydrolase domain / 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
: / Chem-XC3 / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsGrobben, Y. / Uitdehaag, J.C.M. / Tabak, W.W.A. / Zaman, G.J.R.
CitationJournal: J Struct Biol X / Year: 2020
Title: Structural insights into human Arginase-1 pH dependence and its inhibition by the small molecule inhibitor CB-1158.
Authors: Grobben, Y. / Uitdehaag, J.C.M. / Willemsen-Seegers, N. / Tabak, W.W.A. / de Man, J. / Buijsman, R.C. / Zaman, G.J.R.
History
DepositionDec 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,77210
Polymers73,9022
Non-polymers8708
Water6,774376
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,15915
Polymers110,8543
Non-polymers1,30512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6290 Å2
ΔGint-64 kcal/mol
Surface area33840 Å2
MethodPISA
2
B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,15915
Polymers110,8543
Non-polymers1,30512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area6160 Å2
ΔGint-67 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.130, 90.130, 69.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

21B-666-

HOH

31B-672-

HOH

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Components

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


Mass: 36951.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal his tag with thrombin-cleavable linker. Construct was not thrombin-cleaved before crystallization.
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P05089, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XC3 / [(~{E})-3-[(3~{S},4~{R})-4-azanyl-1-[(2~{S})-2-azanylpropanoyl]-4-carboxy-pyrrolidin-3-yl]prop-1-enyl]-tris(oxidanyl)boranium


Mass: 302.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H21BN3O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.2 Å3/Da / Density % sol: 44.23 % / Description: clear rod-like hexagonal crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Crystals were generated from 22.5 % PEG 1500, 0.2 M MIB buffer pH 4.0 (sodium malonate, imidazole and boric acid in a 2:3:3 molar ratio). Crystals were equilibrated to soaking solution (22.5 ...Details: Crystals were generated from 22.5 % PEG 1500, 0.2 M MIB buffer pH 4.0 (sodium malonate, imidazole and boric acid in a 2:3:3 molar ratio). Crystals were equilibrated to soaking solution (22.5 % PEG 1500, 0.2 M MMT buffer pH 9.0 (DL-malic acid, MES, Tris base in a 1:2:2 molar ratio). Subsequently, crystals were gradually soaked for 4 days in soaking solution containing 15 mM compound 3.
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 14, 2017 / Details: transfocator
RadiationMonochromator: diamond beam splitter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.554
11-h,-k,l20.446
ReflectionResolution: 1.61→51.74 Å / Num. obs: 79090 / % possible obs: 96.9 % / Redundancy: 2 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.049 / Rrim(I) all: 0.076 / Net I/σ(I): 6.9
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.658 / Num. unique obs: 3888 / CC1/2: 0.368 / Rpim(I) all: 0.561 / Rrim(I) all: 0.868 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
MOSFLM7.2.0data reduction
Aimless0.7.1data scaling
MOLREP11.6.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q9P

6q9p


Resolution: 1.61→51.74 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.838 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 4105 5.2 %RANDOM
Rwork0.14744 ---
obs0.149 74978 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.684 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å20 Å2
2--3.48 Å20 Å2
3----6.95 Å2
Refinement stepCycle: 1 / Resolution: 1.61→51.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 48 376 5254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194972
X-RAY DIFFRACTIONr_bond_other_d0.0010.024748
X-RAY DIFFRACTIONr_angle_refined_deg1.35626752
X-RAY DIFFRACTIONr_angle_other_deg0.806311054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34824.194186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9115852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6351526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02914
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_it1.2772.3872542
X-RAY DIFFRACTIONr_mcbond_other1.2772.3852541
X-RAY DIFFRACTIONr_mcangle_it1.9913.5783174
X-RAY DIFFRACTIONr_mcangle_other1.9913.5813175
X-RAY DIFFRACTIONr_scbond_it1.2742.5332430
X-RAY DIFFRACTIONr_scbond_other1.2662.5312407
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9993.7323553
X-RAY DIFFRACTIONr_long_range_B_refined3.68331.0675763
X-RAY DIFFRACTIONr_long_range_B_other3.65730.9725725
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free4.9451
X-RAY DIFFRACTIONr_sphericity_bonded5.32553
LS refinement shellResolution: 1.608→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.58 281 -
Rwork0.512 5512 -
obs--96.09 %

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