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- PDB-5ahw: Crystal structure of universal stress protein MSMEG_3811 in compl... -

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Basic information

Entry
Database: PDB / ID: 5ahw
TitleCrystal structure of universal stress protein MSMEG_3811 in complex with cAMP
ComponentsUNIVERSAL STRESS PROTEIN
KeywordsSIGNALING PROTEIN / RV1636 HOMOLOG / USP TYPE 1 HOMODIMER / WALKER A-LIKE MOTIF / ATP-BINDING MOTIF
Function / homology
Function and homology information


Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Chem-POG / Universal stress protein family protein, putative
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS STR. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsAdolph, R.S. / Kleinboelting, S. / Weyand, M. / Steegborn, C.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Universal Stress Protein (Usp) in Mycobacteria Binds Camp
Authors: Banerjee, A. / Adolph, R.S. / Gopalakrishnapai, J. / Kleinboelting, S. / Emmerich, C. / Steegborn, C. / Visweswariah, S.S.
History
DepositionFeb 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: UNIVERSAL STRESS PROTEIN
B: UNIVERSAL STRESS PROTEIN
C: UNIVERSAL STRESS PROTEIN
D: UNIVERSAL STRESS PROTEIN
E: UNIVERSAL STRESS PROTEIN
F: UNIVERSAL STRESS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,33124
Polymers91,3396
Non-polymers3,99218
Water4,486249
1
A: UNIVERSAL STRESS PROTEIN
B: UNIVERSAL STRESS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4649
Polymers30,4462
Non-polymers1,0187
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: UNIVERSAL STRESS PROTEIN
D: UNIVERSAL STRESS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1468
Polymers30,4462
Non-polymers1,7006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: UNIVERSAL STRESS PROTEIN
F: UNIVERSAL STRESS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7217
Polymers30,4462
Non-polymers1,2755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-39.8 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.530, 126.780, 151.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1149-

SO4

21A-2012-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
UNIVERSAL STRESS PROTEIN / / HYPOTHETICAL PROTEIN MSMEG_3811


Mass: 15223.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS STR. MC2 155 (bacteria)
Plasmid: PPROEX-HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QYW6

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Non-polymers , 5 types, 267 molecules

#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-POG / (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL / POLYPROPYLENE GLYCOL / HEPTAPROPYLENE GLYCOL / Polypropylene glycol


Mass: 424.569 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H44O8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.04 Å3/Da / Density % sol: 39.9 % / Description: NONE
Crystal growpH: 6
Details: PROTEIN WAS COCRYSTALLIZED WITH 5 MM CAMP IN 0.1 M MES, PH 6.0; 1.9 M AMMONIUM SULFATE; 6 % (V/V) POLYPROPYLENGLYCOL 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2013 / Details: COLLIMATOR
RadiationMonochromator: SI111-DCM WITH SAGITTAL BENDER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.15→48.64 Å / Num. obs: 43084 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.8 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z08

2z08


Resolution: 2.15→48.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.713 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 2155 5 %RANDOM
Rwork0.17875 ---
obs0.18158 40929 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.15→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5579 0 230 249 6058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195890
X-RAY DIFFRACTIONr_bond_other_d0.0010.025807
X-RAY DIFFRACTIONr_angle_refined_deg1.9012.0238066
X-RAY DIFFRACTIONr_angle_other_deg0.863313279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89423.961207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47315884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6851547
X-RAY DIFFRACTIONr_chiral_restr0.1010.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021172
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9672.5073095
X-RAY DIFFRACTIONr_mcbond_other1.9662.5063094
X-RAY DIFFRACTIONr_mcangle_it3.0543.7373852
X-RAY DIFFRACTIONr_mcangle_other3.0543.7373853
X-RAY DIFFRACTIONr_scbond_it2.8613.0632795
X-RAY DIFFRACTIONr_scbond_other2.8613.0642796
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3774.4394210
X-RAY DIFFRACTIONr_long_range_B_refined7.41922.3166617
X-RAY DIFFRACTIONr_long_range_B_other7.41822.3226618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 157 -
Rwork0.314 2968 -
obs--98.46 %
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)
13.159-1.0003-1.12412.79730.2862.7660.1370.4309-0.0464-0.6345-0.11270.0105-0.0839-0.2583-0.02430.48430.0317-0.03320.26570.02850.0106-1.0334-9.031113.8435
22.269-0.00240.13042.17320.12481.24220.03460.01070.2231-0.0698-0.0115-0.2972-0.20040.1388-0.02310.3422-0.03450.02250.1285-0.00130.06314.5406-5.202930.1722
31.5298-0.9577-0.59013.4871.37642.37380.0392-0.1779-0.06030.4918-0.07720.5815-0.0647-0.1220.0380.2604-0.04120.12880.1391-0.00670.123916.38735.25858.1775
42.08830.70510.22083.58090.48761.73220.0186-0.0296-0.26010.13-0.04130.22840.1963-0.13440.02260.1844-0.05520.00420.053-0.00780.065324.020514.485645.8442
52.3233-0.0410.74181.47310.59973.24170.13130.53930.0281-0.356-0.01570.05380.33270.058-0.11550.39960.0012-0.06560.27190.01510.014236.396620.051810.5669
62.2547-0.09730.48852.74330.44263.81270.12550.25550.3877-0.0456-0.23570.69270.0603-0.72360.11020.2081-0.0274-0.03290.35810.03930.266718.644531.088219.4077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 147
2X-RAY DIFFRACTION2B2 - 147
3X-RAY DIFFRACTION3C2 - 147
4X-RAY DIFFRACTION4D2 - 147
5X-RAY DIFFRACTION5E2 - 147
6X-RAY DIFFRACTION6F2 - 147

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