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- PDB-4rzb: The structure of N-formimino-L-Glutamate Iminohydrolase from Pseu... -

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Basic information

Entry
Database: PDB / ID: 4rzb
TitleThe structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa complexed with N-formimino-L-Aspartate, SOAKED WITH MERCURY
ComponentsN-formimino-L-Glutamate Iminohydrolase
KeywordsHYDROLASE / amidohydrolase fold / N-formimino-L-Glutamate Iminohydrolase / N-formimino-L-Aspartate
Function / homology
Function and homology information


formimidoylglutamate deiminase / formimidoylglutamate deiminase activity / L-histidine catabolic process / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / deaminase activity / metal ion binding / cytosol
Similarity search - Function
Formiminoglutamate deiminase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...Formiminoglutamate deiminase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / N-[(E)-iminomethyl]-L-aspartic acid / Formimidoylglutamate deiminase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.863 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Marti-Arbona, R. / Raushel, F.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2015
Title: Structure of N-Formimino-l-glutamate Iminohydrolase from Pseudomonas aeruginosa.
Authors: Fedorov, A.A. / Marti-Arbona, R. / Nemmara, V.V. / Hitchcock, D. / Fedorov, E.V. / Almo, S.C. / Raushel, F.M.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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_ptnr1_label_alt_id / _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_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: N-formimino-L-Glutamate Iminohydrolase
B: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,93817
Polymers98,8072
Non-polymers2,13115
Water16,159897
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-220 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.560, 141.831, 86.415
Angle α, β, γ (deg.)90.00, 107.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-741-

HOH

21A-908-

HOH

31A-1061-

HOH

41B-689-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-formimino-L-Glutamate Iminohydrolase


Mass: 49403.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA5106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HU77

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Non-polymers , 6 types, 912 molecules

#2: Chemical ChemComp-NFQ / N-[(E)-iminomethyl]-L-aspartic acid / N-formimino-L-Aspartate


Mass: 160.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8N2O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 897 / 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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.4M sodium sulfate, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.863→40.986 Å / Num. all: 97124 / Num. obs: 97124 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.863→40.986 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1764 2925 3.01 %RANDOM
Rwork0.1596 ---
all0.1602 97124 --
obs0.1602 97124 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.863→40.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 56 897 7875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077211
X-RAY DIFFRACTIONf_angle_d1.0619798
X-RAY DIFFRACTIONf_dihedral_angle_d12.9592611
X-RAY DIFFRACTIONf_chiral_restr0.0771048
X-RAY DIFFRACTIONf_plane_restr0.0051316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8626-1.89320.29971310.25184351X-RAY DIFFRACTION96
1.8932-1.92580.24451340.21524464X-RAY DIFFRACTION100
1.9258-1.96080.23611300.20274484X-RAY DIFFRACTION100
1.9608-1.99850.20611500.19154472X-RAY DIFFRACTION100
1.9985-2.03930.19921310.18574491X-RAY DIFFRACTION100
2.0393-2.08370.21651390.17774489X-RAY DIFFRACTION100
2.0837-2.13210.20921510.17244442X-RAY DIFFRACTION100
2.1321-2.18550.20031520.17074485X-RAY DIFFRACTION100
2.1855-2.24450.18071480.17214476X-RAY DIFFRACTION100
2.2445-2.31060.1911390.16584465X-RAY DIFFRACTION100
2.3106-2.38520.17721310.16444487X-RAY DIFFRACTION100
2.3852-2.47040.17971220.15774525X-RAY DIFFRACTION100
2.4704-2.56930.18621550.16894475X-RAY DIFFRACTION100
2.5693-2.68620.19011440.16394471X-RAY DIFFRACTION100
2.6862-2.82780.1891350.16124530X-RAY DIFFRACTION100
2.8278-3.00490.18661390.16034478X-RAY DIFFRACTION100
3.0049-3.23680.18261590.1624482X-RAY DIFFRACTION100
3.2368-3.56240.14671510.14344471X-RAY DIFFRACTION100
3.5624-4.07750.14561480.13444522X-RAY DIFFRACTION100
4.0775-5.13560.13231100.1274566X-RAY DIFFRACTION100
5.1356-40.99620.14551260.15424573X-RAY DIFFRACTION100
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)
10.77050.00580.37420.78860.2580.98690.08140.0734-0.0730.05470.0228-0.07680.11620.0535-0.0910.1168-0.0079-0.03290.09580.0070.124593.092715.1633107.3406
20.6187-0.3016-0.04071.01150.42730.9363-0.0116-0.00490.1433-0.03060.0381-0.2072-0.08620.0796-0.00020.1038-0.0281-0.01140.10250.02380.178291.293749.4945112.3097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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