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- PDB-3mdw: The structure of N-formimino-L-Glutamate Iminohydrolase from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3mdw
TitleThe structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa complexed with N-formimino-L-Aspartate
ComponentsN-formimino-L-Glutamate Iminohydrolase
KeywordsHYDROLASE / Aminohydrolase family / N-formimino-L-Glutamate Iminohydrolase
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 / PHOSPHATE ION / Formimidoylglutamate deiminase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8979 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
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Jan 28, 2015Group: Database references
Revision 1.4Feb 11, 2015Group: Database references
Revision 1.5Feb 21, 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_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_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.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
C: N-formimino-L-Glutamate Iminohydrolase
D: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,79615
Polymers197,6154
Non-polymers1,18111
Water18,9881054
1
A: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7214
Polymers49,4041
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6293
Polymers49,4041
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7214
Polymers49,4041
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7244
Polymers49,4041
Non-polymers3213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: N-formimino-L-Glutamate Iminohydrolase
B: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3517
Polymers98,8072
Non-polymers5435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-13 kcal/mol
Surface area29730 Å2
MethodPISA
6
C: N-formimino-L-Glutamate Iminohydrolase
D: N-formimino-L-Glutamate Iminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4468
Polymers98,8072
Non-polymers6386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-17 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)304.046, 67.247, 98.229
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 49403.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA5106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HU77

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Non-polymers , 5 types, 1065 molecules

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


Mass: 160.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H8N2O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1054 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.4M Sodium Phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.0

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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: Apr 3, 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: 1.8979→39.43 Å / Num. all: 148848 / Num. obs: 148848 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8979→39.427 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 7465 5.02 %RANDOM
Rwork0.1697 ---
all0.1714 148848 --
obs0.1714 148848 94.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.2306 Å20 Å2-0.1447 Å2
2--13.3094 Å2-0 Å2
3----6.0024 Å2
Refinement stepCycle: LAST / Resolution: 1.8979→39.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13788 0 65 1054 14907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714152
X-RAY DIFFRACTIONf_angle_d1.04219203
X-RAY DIFFRACTIONf_dihedral_angle_d16.3595101
X-RAY DIFFRACTIONf_chiral_restr0.0752061
X-RAY DIFFRACTIONf_plane_restr0.0052575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8979-1.91950.30681540.2552917X-RAY DIFFRACTION58
1.9195-1.94210.30071720.24583349X-RAY DIFFRACTION69
1.9421-1.96580.27152020.22883652X-RAY DIFFRACTION74
1.9658-1.99070.29021920.22563864X-RAY DIFFRACTION78
1.9907-2.01690.26122180.21594134X-RAY DIFFRACTION84
2.0169-2.04450.26582230.20624437X-RAY DIFFRACTION89
2.0445-2.07370.23182390.18134623X-RAY DIFFRACTION94
2.0737-2.10460.22362670.17534865X-RAY DIFFRACTION98
2.1046-2.13750.212560.17684962X-RAY DIFFRACTION100
2.1375-2.17260.22212470.1784971X-RAY DIFFRACTION100
2.1726-2.210.2292760.16524862X-RAY DIFFRACTION100
2.21-2.25020.22092690.1635000X-RAY DIFFRACTION100
2.2502-2.29350.22762660.16224928X-RAY DIFFRACTION100
2.2935-2.34030.21312500.16464945X-RAY DIFFRACTION100
2.3403-2.39120.21322980.16684932X-RAY DIFFRACTION100
2.3912-2.44680.21542580.1674909X-RAY DIFFRACTION100
2.4468-2.5080.22032650.17894974X-RAY DIFFRACTION100
2.508-2.57580.22762800.18254948X-RAY DIFFRACTION100
2.5758-2.65150.2362550.17434957X-RAY DIFFRACTION100
2.6515-2.73710.20212630.17114982X-RAY DIFFRACTION100
2.7371-2.83490.20362620.17994955X-RAY DIFFRACTION100
2.8349-2.94840.21152590.17024984X-RAY DIFFRACTION100
2.9484-3.08250.21212780.17164966X-RAY DIFFRACTION100
3.0825-3.2450.19432380.16874994X-RAY DIFFRACTION100
3.245-3.44820.17762490.16414992X-RAY DIFFRACTION100
3.4482-3.71420.18172530.15165041X-RAY DIFFRACTION100
3.7142-4.08760.17672880.14374969X-RAY DIFFRACTION100
4.0876-4.67830.13592740.1345003X-RAY DIFFRACTION100
4.6783-5.8910.19152450.15965083X-RAY DIFFRACTION100
5.891-39.43580.16752690.1685185X-RAY DIFFRACTION100

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