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- PDB-3pzl: The crystal structure of agmatine ureohydrolase of Thermoplasma v... -

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Basic information

Entry
Database: PDB / ID: 3pzl
TitleThe crystal structure of agmatine ureohydrolase of Thermoplasma volcanium
ComponentsAgmatine ureohydrolase
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Agmatinase-related / 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
: / Agmatine ureohydrolase
Similarity search - Component
Biological speciesThermoplasma volcanium GSS1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of agmatine ureohydrolase of Thermoplasma volcanium
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_seq_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: Agmatine ureohydrolase
B: Agmatine ureohydrolase
C: Agmatine ureohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4359
Polymers106,1053
Non-polymers3306
Water90150
1
A: Agmatine ureohydrolase
B: Agmatine ureohydrolase
C: Agmatine ureohydrolase
hetero molecules

A: Agmatine ureohydrolase
B: Agmatine ureohydrolase
C: Agmatine ureohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,86918
Polymers212,2106
Non-polymers65912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area22750 Å2
ΔGint-174 kcal/mol
Surface area57690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.139, 95.139, 198.375
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Agmatine ureohydrolase


Mass: 35368.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium GSS1 (archaea) / Strain: ATCC 51530 / Gene: TV0538, TVG0528110 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codon+RIL(p) / References: UniProt: Q97BB8
#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.: 50 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M BICINE pH 9.0, 2% v/v 1,4-Dioxane, 10% w/v PEG 20,000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→83.4 Å / Num. obs: 26146 / % possible obs: 93.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.6 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 15.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 21.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4199 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→82.39 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.898 / SU B: 31.544 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27105 1398 5.1 %RANDOM
Rwork0.21954 ---
obs0.22208 26146 93.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.624 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å21.24 Å20 Å2
2--2.48 Å20 Å2
3----3.72 Å2
Refinement stepCycle: LAST / Resolution: 2.7→82.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6840 0 6 50 6896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9729409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18323.436326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.728151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.91557
X-RAY DIFFRACTIONr_chiral_restr0.0920.21035
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215305
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9721.54329
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52226977
X-RAY DIFFRACTIONr_scbond_it2.53832638
X-RAY DIFFRACTIONr_scangle_it3.8694.52432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 106 -
Rwork0.239 2015 -
obs-4199 100 %
Refinement TLS params.Method: refined / Origin x: -14.0693 Å / Origin y: -56.1216 Å / Origin z: -7.9033 Å
111213212223313233
T0.0556 Å20.0783 Å2-0.0102 Å2-0.135 Å20.0018 Å2--0.0556 Å2
L0.2427 °2-0.0014 °2-0.2813 °2-0.1853 °20.1598 °2--0.752 °2
S-0.0221 Å °0.0051 Å °-0.037 Å °0.0056 Å °-0.0106 Å °-0.0263 Å °0.0858 Å °0.1307 Å °0.0327 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 302
2X-RAY DIFFRACTION1B13 - 305
3X-RAY DIFFRACTION1C13 - 302

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