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- PDB-3n1s: Crystal structure of wild type ecHint GMP complex -

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Basic information

Entry
Database: PDB / ID: 3n1s
TitleCrystal structure of wild type 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: 1.45 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
I: HIT-like protein hinT
J: HIT-like protein hinT
M: HIT-like protein hinT
N: HIT-like protein hinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,52441
Polymers106,0668
Non-polymers4,45733
Water19,2401068
1
A: HIT-like protein hinT
B: HIT-like protein hinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,80213
Polymers26,5172
Non-polymers1,28511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-25 kcal/mol
Surface area10520 Å2
MethodPISA
2
E: HIT-like protein hinT
F: HIT-like protein hinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3676
Polymers26,5172
Non-polymers8514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-34 kcal/mol
Surface area10460 Å2
MethodPISA
3
I: HIT-like protein hinT
J: HIT-like protein hinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,61510
Polymers26,5172
Non-polymers1,0998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-23 kcal/mol
Surface area10660 Å2
MethodPISA
4
M: HIT-like protein hinT
N: HIT-like protein hinT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,74012
Polymers26,5172
Non-polymers1,22310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-24 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.183, 65.298, 99.122
Angle α, β, γ (deg.)90.00, 109.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HIT-like protein hinT


Mass: 13258.262 Da / Num. of mol.: 8
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.: 8 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1068 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40% PEG 20000, 0.1M Magnesium Acetate, 0.1M Sodium Acetate, 20 mM Tris, pH 7.0, 1mM 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: 1.35→38 Å / Num. all: 222096 / Num. obs: 149986 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.115 / Net I/σ(I): 5.3
Reflection shellResolution: 1.35→1.45 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.2 / Num. unique all: 17208 / Rsym value: 0.4 / % possible all: 77.7

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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 1AV5

1av5


Resolution: 1.45→37.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.299 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20939 7983 5.1 %RANDOM
Rwork0.17744 ---
obs0.17904 149986 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.504 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.163 Å
Refinement stepCycle: LAST / Resolution: 1.45→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7277 0 292 1068 8637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228156
X-RAY DIFFRACTIONr_angle_refined_deg1.517211155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93751054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23524.04354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.376151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7841558
X-RAY DIFFRACTIONr_chiral_restr0.0990.21283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026116
X-RAY DIFFRACTIONr_nbd_refined0.2220.24083
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2850
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.2219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.279
X-RAY DIFFRACTIONr_mcbond_it0.7961.55117
X-RAY DIFFRACTIONr_mcangle_it1.21828082
X-RAY DIFFRACTIONr_scbond_it1.93733465
X-RAY DIFFRACTIONr_scangle_it2.8514.53031
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 627 -
Rwork0.232 10807 -
obs--97.43 %

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