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- PDB-5f2h: 2.75 Angstrom resolution crystal structure of uncharacterized pro... -

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Basic information

Entry
Database: PDB / ID: 5f2h
Title2.75 Angstrom resolution crystal structure of uncharacterized protein from Bacillus cereus ATCC 10987
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Bacillus cereus ATCC 10987 / PSI-Biology / Human Microbiome / Metagenomics degradome representatives / Structural Genomics / Midwest Center for Structural Genomics / MCSG
Function / homologyA/B hydrolase-like, N-terminal domain / : / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold / hydrolase activity / Phospholipase/carboxylesterase/thioesterase domain-containing protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsHalavaty, A.S. / Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: 2.75 Angstrom resolution crystal structure of uncharacterized protein from Bacillus cereus ATCC 10987
Authors: Halavaty, A.S. / Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9425
Polymers74,5762
Non-polymers3663
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-14 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.067, 42.176, 106.032
Angle α, β, γ (deg.)90.00, 92.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 5 - 310 / Label seq-ID: 8 - 313

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Uncharacterized protein


Mass: 37287.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / NRS 248 / Gene: BCE_2095 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) magic / References: UniProt: Q739P5
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (SeMet): 8.9 mg/ml in 10 mM Tris-HCl pH 8.3 0.25 M NaCl, 5 mM BME Crystallization: The Classics II D7(43): 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG3350 Cryo: Crystallization condition soak

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 16616 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 69.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 31
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
BLU-MAXdata collection
HKL-3000data scaling
HKL-3000phasing
Cootmodel building
ARPmodel building
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.75→27.17 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.895 / SU B: 42.683 / SU ML: 0.391 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29052 836 5 %RANDOM
Rwork0.23019 ---
obs0.23319 15767 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 83.11 Å2
Baniso -1Baniso -2Baniso -3
1-10.46 Å20 Å2-2.32 Å2
2--2.73 Å20 Å2
3----13.05 Å2
Refinement stepCycle: 1 / Resolution: 2.75→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 24 20 5071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195163
X-RAY DIFFRACTIONr_bond_other_d0.0030.024825
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9626963
X-RAY DIFFRACTIONr_angle_other_deg0.92311166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2675609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.41225.839274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.28115899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1291510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025805
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021161
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17533 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.754→2.825 Å
RfactorNum. reflection% reflection
Rfree0.344 57 5 %
Rwork0.367 1103 -
obs--94.85 %
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)
11.6529-0.72950.82081.29250.13495.4879-0.1773-0.3361-0.03040.23440.25430.15140.3966-0.4609-0.07710.1025-0.03470.08050.29730.01130.561857.83285.219995.5826
22.32160.2752-1.79034.35671.05118.31530.2038-0.15960.29920.40220.38090.1343-0.325-0.0984-0.58460.07990.07410.07420.16210.00080.489835.668911.738534.9408
31.04720.4185-0.57621.22371.26126.952-0.08020.24410.1475-0.11930.4699-0.26390.4490.8527-0.38970.07560.00440.04960.2346-0.06360.466944.31032.322211.4338
42.625-0.1761-0.75643.8717-0.325.1938-0.00660.37590.2362-0.26580.0756-0.2829-0.2150.1709-0.0690.0463-0.08660.03910.3348-0.02640.531764.268115.072770.4624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 127
2X-RAY DIFFRACTION2A128 - 310
3X-RAY DIFFRACTION3B5 - 127
4X-RAY DIFFRACTION4B128 - 312

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