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- PDB-4fpw: Crystal Structure of CalU16 from Micromonospora echinospora. Nort... -

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Basic information

Entry
Database: PDB / ID: 4fpw
TitleCrystal Structure of CalU16 from Micromonospora echinospora. Northeast Structural Genomics Consortium Target MiR12.
ComponentsCalU16
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Northeast Structural Genomics Consortium / NESG / CalU16
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / CalU16
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSeetharaman, J. / Lew, S. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Phillips Jr., G.N. / Kennedy, M.A. / Montelione, G.T. / Hunt, J.F. ...Seetharaman, J. / Lew, S. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Phillips Jr., G.N. / Kennedy, M.A. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19.
Authors: Elshahawi, S.I. / Ramelot, T.A. / Seetharaman, J. / Chen, J. / Singh, S. / Yang, Y. / Pederson, K. / Kharel, M.K. / Xiao, R. / Lew, S. / Yennamalli, R.M. / Miller, M.D. / Wang, F. / Tong, L. ...Authors: Elshahawi, S.I. / Ramelot, T.A. / Seetharaman, J. / Chen, J. / Singh, S. / Yang, Y. / Pederson, K. / Kharel, M.K. / Xiao, R. / Lew, S. / Yennamalli, R.M. / Miller, M.D. / Wang, F. / Tong, L. / Montelione, G.T. / Kennedy, M.A. / Bingman, C.A. / Zhu, H. / Phillips, G.N. / Thorson, J.S.
History
DepositionJun 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalU16
B: CalU16


Theoretical massNumber of molelcules
Total (without water)40,4712
Polymers40,4712
Non-polymers00
Water2,306128
1
A: CalU16


Theoretical massNumber of molelcules
Total (without water)20,2361
Polymers20,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CalU16


Theoretical massNumber of molelcules
Total (without water)20,2361
Polymers20,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.852, 51.852, 305.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 180
2010B5 - 180

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Components

#1: Protein CalU16


Mass: 20235.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calU16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KNE9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7
Details: 2.9 M Sodium malonate pH 7, Microbatch under oil, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.979
NSLS X6A2
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDApr 12, 2012
2
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.499
11K, H, -L20.501
ReflectionResolution: 2.5→50 Å / Num. all: 21977 / Num. obs: 21977 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.063 / Rsym value: 0.057 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.225 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.91 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 18.134 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28163 794 5 %RANDOM
Rwork0.24063 ---
obs0.24263 15160 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.644 Å2
Baniso -1Baniso -2Baniso -3
1-33.44 Å20 Å20 Å2
2--33.44 Å20 Å2
3----66.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 0 128 2625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192546
X-RAY DIFFRACTIONr_bond_other_d0.0020.022384
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9683442
X-RAY DIFFRACTIONr_angle_other_deg0.81235481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2265314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43823.281128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75415408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8681530
X-RAY DIFFRACTIONr_chiral_restr0.0770.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 149 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.24 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 44 -
Rwork0.325 1128 -
obs--99.15 %
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)
12.70380.4318-0.05151.0925-0.5011.60990.1934-0.136-0.03990.0011-0.1357-0.05160.0624-0.0267-0.05770.20180.0683-0.01050.0626-0.02570.232226.0578-13.5533-4.3343
20.7127-0.1763-0.48281.9968-0.54591.95430.0022-0.181-0.0513-0.34430.0802-0.0364-0.11860.0467-0.08240.1001-0.00010.0030.2975-0.01730.289124.872-15.331728.1748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 180
2X-RAY DIFFRACTION2B5 - 180

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