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- PDB-3n1t: Crystal structure of the H101A mutant ecHint GMP complex -

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Basic information

Entry
Database: PDB / ID: 3n1t
TitleCrystal structure of the H101A mutant ecHint GMP complex
ComponentsHIT-like protein hinT
KeywordsHYDROLASE / histidine triad nucleotide binding protein / Hint / GMP
Function / homology
Function and homology information


D-alanine catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / nucleotide binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Purine nucleoside phosphoramidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.716 Å
AuthorsCody, V.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Probing the Impact of the echinT C-Terminal Domain on Structure and Catalysis.
Authors: Bardaweel, S. / Pace, J. / Chou, T.F. / Cody, V. / Wagner, C.R.
History
DepositionMay 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HIT-like protein hinT
B: HIT-like protein hinT
E: HIT-like protein hinT
F: HIT-like protein hinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2188
Polymers52,7654
Non-polymers1,4534
Water5,711317
1
A: HIT-like protein hinT
B: HIT-like protein hinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1094
Polymers26,3822
Non-polymers7262
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-34 kcal/mol
Surface area10040 Å2
MethodPISA
2
E: HIT-like protein hinT
F: HIT-like protein hinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1094
Polymers26,3822
Non-polymers7262
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-39 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.327, 64.066, 74.750
Angle α, β, γ (deg.)90.00, 109.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HIT-like protein hinT


Mass: 13191.192 Da / Num. of mol.: 4 / Mutation: H101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BB2 / Plasmid: pB429 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACE7
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40% PEG 20000, 0.1M Magnesium Acetate, 0.1M Sodium Acetate, 20mM Tris pH 7.0, 1 mM EDTA, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.975 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 6, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.716→37.7 Å / Num. all: 41405 / Num. obs: 41372 / % possible obs: 88.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.716→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.47 / % possible all: 25.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N1S

3n1s


Resolution: 1.716→35.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.382 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24543 2075 5 %RANDOM
Rwork0.19387 ---
obs0.19644 39308 87.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.767 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.212 Å
Refinement stepCycle: LAST / Resolution: 1.716→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 96 317 3973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223731
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9975086
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75224165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79915623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7621528
X-RAY DIFFRACTIONr_chiral_restr0.2440.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022782
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2760.21933
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22554
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0341.52379
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5823706
X-RAY DIFFRACTIONr_scbond_it2.86131568
X-RAY DIFFRACTIONr_scangle_it4.1464.51380
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.716→1.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 47 -
Rwork0.292 1004 -
obs--30.18 %

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