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- PDB-4gn0: De novo phasing of a Hamp-complex using an improved Arcimboldo method -

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Basic information

Entry
Database: PDB / ID: 4gn0
TitleDe novo phasing of a Hamp-complex using an improved Arcimboldo method
ComponentsHamp domain of AF1503
KeywordsSIGNALING PROTEIN / Four helix bundle / Hamp domain / Transmembrane signalling
Function / homology
Function and homology information


signal transduction / identical protein binding / membrane / metal ion binding
Similarity search - Function
hypothetical protein mp506/mpn330, domain 1 / hypothetical protein mp506/mpn330, domain 1 - #10 / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Helix non-globular / Special
Similarity search - Domain/homology
HAMP domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.75 Å
AuthorsHulko, M. / Ursinus, A. / Bar, K. / Martin, J. / Zeth, K. / Lupas, A.N.
CitationJournal: Nat.Methods / Year: 2013
Title: Exploiting tertiary structure through local folds for crystallographic phasing.
Authors: Sammito, M. / Millan, C. / Rodriguez, D.D. / de Ilarduya, I.M. / Meindl, K. / De Marino, I. / Petrillo, G. / Buey, R.M. / de Pereda, J.M. / Zeth, K. / Sheldrick, G.M. / Uson, I.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Jan 22, 2014Group: Structure summary
Revision 1.4Mar 19, 2014Group: Structure summary
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Hamp domain of AF1503
B: Hamp domain of AF1503
C: Hamp domain of AF1503
D: Hamp domain of AF1503
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5845
Polymers45,5594
Non-polymers241
Water6,720373
1
A: Hamp domain of AF1503
C: Hamp domain of AF1503
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8043
Polymers22,7802
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-29 kcal/mol
Surface area14470 Å2
MethodPISA
2
B: Hamp domain of AF1503
D: Hamp domain of AF1503


Theoretical massNumber of molelcules
Total (without water)22,7802
Polymers22,7802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-35 kcal/mol
Surface area13850 Å2
MethodPISA
3
A: Hamp domain of AF1503
C: Hamp domain of AF1503
hetero molecules

B: Hamp domain of AF1503
D: Hamp domain of AF1503


Theoretical massNumber of molelcules
Total (without water)45,5845
Polymers45,5594
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area12970 Å2
ΔGint-145 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.115, 48.077, 95.262
Angle α, β, γ (deg.)90.00, 98.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hamp domain of AF1503


Mass: 11389.803 Da / Num. of mol.: 4 / Fragment: UNP residues 31-338
Mutation: Y255K, Y256N, A257L, G259T, I260L, A263D, I264R, I266E, V267Q, F268I, I270N, V271D, V274S, F275T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1503 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O28769
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.2 Å3/Da / Density % sol: 43.98 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 39972 / Biso Wilson estimate: 22.04 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.75→41.93 Å / Cor.coef. Fo:Fc: 0.9299 / Cor.coef. Fo:Fc free: 0.9096 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 2005 5.02 %RANDOM
Rwork0.1926 ---
obs0.1942 39972 99.5 %-
Displacement parametersBiso mean: 26.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.5338 Å20 Å2-7.4266 Å2
2---0.3241 Å20 Å2
3---1.8579 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: LAST / Resolution: 1.75→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 1 373 3503
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013138HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994237HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1190SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes436HARMONIC5
X-RAY DIFFRACTIONt_it3138HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion16.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion472SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4201SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2696 143 4.85 %
Rwork0.216 2803 -
all0.2185 2946 -
obs--99.5 %

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