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- PDB-4m6d: Crystal structure of the aptamer minF-lysozyme complex. -

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Basic information

Entry
Database: PDB / ID: 4m6d
TitleCrystal structure of the aptamer minF-lysozyme complex.
Components
  • Lysozyme C
  • aptamer
KeywordsHydrolase/RNA / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium / Hydrolase-RNA complex
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å
AuthorsMalashkevich, V.N. / Padlan, F.C. / Toro, R. / Girvin, M. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of the aptamer minF-lysozyme complex.
Authors: Malashkevich, V.N. / Padlan, F.C. / Toro, R. / Girvin, M. / Almo, S.C.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
B: aptamer
C: Lysozyme C
D: aptamer
E: Lysozyme C
F: aptamer
G: Lysozyme C
H: aptamer
I: Lysozyme C
J: aptamer
K: Lysozyme C
L: aptamer


Theoretical massNumber of molelcules
Total (without water)173,11712
Polymers173,11712
Non-polymers00
Water1,24369
1
A: Lysozyme C
B: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lysozyme C
D: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Lysozyme C
F: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Lysozyme C
H: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Lysozyme C
J: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Lysozyme C
L: aptamer


Theoretical massNumber of molelcules
Total (without water)28,8532
Polymers28,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.914, 132.289, 131.539
Angle α, β, γ (deg.)118.59, 96.39, 96.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ, lyz1 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: P00698, lysozyme
#2: RNA chain
aptamer /


Mass: 14521.679 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: minF
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M Malonic Acid, 0.15 M Ammonium Citrate Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic, Final pH 7. ...Details: 1.1M Malonic Acid, 0.15 M Ammonium Citrate Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic, Final pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 18, 2013
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.351
11-H, H+K+L, -L20.014
11-H, -L, -K30.015
11H, L, -H-K-L40.344
11H, -H-K-L, K50.267
11-H, -K, H+K+L60.009
ReflectionResolution: 2.68→50 Å / Num. obs: 67209 / % possible obs: 94.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.751.80.629190.9
2.75-2.81.80.571191.5
2.8-2.851.80.491192.6
2.85-2.911.80.38192.1
2.91-2.971.80.358193.3
2.97-3.041.80.278195.7
3.04-3.121.80.234194.6
3.12-3.21.90.189195.6
3.2-3.31.90.153197.1
3.3-3.41.90.127195.1
3.4-3.521.90.117198.3
3.52-3.661.90.103195.7
3.66-3.831.90.088197.6
3.83-4.031.90.07195.5
4.03-4.291.90.061196.7
4.29-4.621.90.055195.6
4.62-5.081.90.051196.7
5.08-5.811.90.047196.8
5.81-7.321.90.042195.6
7.32-501.90.037190.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.41 Å37.82 Å
Translation6.41 Å37.82 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M4O

4m4o


Resolution: 2.68→38.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0 / SU B: 20.942 / SU ML: 0.198 / SU R Cruickshank DPI: 0.1634 / Cross valid method: THROUGHOUT / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. ORIGINALLY DATA WERE PROCESSED IN H3, WITH ONE RNA:PROTEIN HETERDIMER PER ASYMMETRIC UNIT. BUT REFINEMENT STATISTICS WERE AROUND 0.32/0.36. ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. ORIGINALLY DATA WERE PROCESSED IN H3, WITH ONE RNA:PROTEIN HETERDIMER PER ASYMMETRIC UNIT. BUT REFINEMENT STATISTICS WERE AROUND 0.32/0.36. THE REFINEMENT STATISTICS ARE MUCH BETTER WHEN DATA PROCESSED IN P1, INDICATING DIFFERENCES BETWEEN SUBUNITS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3007 5.3 %RANDOM
Rwork0.16549 ---
obs0.16832 53394 79.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 122.84 Å2
Baniso -1Baniso -2Baniso -3
1--33.08 Å2-1.5 Å2-4.37 Å2
2--74.15 Å2-12.52 Å2
3----41.07 Å2
Refinement stepCycle: LAST / Resolution: 2.68→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6006 5357 0 69 11432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01512133
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.57217653
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80923.131297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.93615996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6771563
X-RAY DIFFRACTIONr_chiral_restr0.0940.21864
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027368
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.26311.3573090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8783852
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.99515.2129043
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_restr8.222312133
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded53.84511360
LS refinement shellResolution: 2.685→2.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 13 -
Rwork0.196 338 -
obs--6.64 %
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)
11.17790.77230.32132.36960.74970.29320.0506-0.0258-0.135-0.0105-0.0091-0.37710.07660.042-0.04150.22790.07050.03420.4258-0.09970.3336-2.969-37.59-29.807
22.11680.18040.33673.837-0.63882.9442-0.52410.68050.6364-0.2013-0.31890.4377-0.08430.15620.8430.5224-0.008-0.18930.947-0.0850.5589-25.676-48.064-56.111
31.6210.62320.5333.78140.71820.6339-0.067-0.10640.22430.0710.03590.3319-0.1358-0.12350.0310.21030.04330.05620.4162-0.12980.3367-22.025-17.267-18.462
46.29883.0799-2.94723.2331-1.18941.443-0.0655-0.3072-0.2807-0.5221-0.1539-0.3671-0.10250.1430.21940.47450.0718-0.18160.7015-0.11780.61611.00710.776-22.45
51.6284-0.66890.62922.4575-1.23440.927-0.03410.18710.12690.0654-0.1638-0.4533-0.1410.17650.19790.26660.00050.01010.46080.04750.3603-2.78744.493-19.824
61.064-0.5989-0.5573.12150.03370.3951-0.1903-0.00330.16140.56870.14730.47930.029-0.08440.0430.54050.0621-0.10880.6044-0.13690.6229-25.51272.576-15.698
71.1365-1.25010.9032.589-1.65211.65560.1530.0185-0.2627-0.02440.08340.3959-0.013-0.0706-0.23640.2431-0.0097-0.0280.47740.06380.3609-21.96824.425-8
81.4395-0.10441.34611.4847-0.61441.5729-0.15060.04210.41810.0507-0.1739-0.3506-0.10110.14910.32440.64420.08240.01750.52210.05930.47031.01213.98818.214
91.41340.0611-0.53460.09960.33591.5490.039-0.0827-0.05940.03030.0374-0.03020.06390.1-0.07640.28020.0192-0.02080.465-0.01240.0183-2.816-4.69346.028
102.991-0.1716-1.24721.0589-0.60631.2196-0.3525-0.0974-0.4556-0.28540.30110.30610.46620.05110.05140.47220.07490.00490.6140.09860.154-25.558-22.18968.174
111.4143-0.0733-1.1640.44190.44592.89250.1430.14340.0249-0.08240.0288-0.0131-0.111-0.181-0.17180.2110.0244-0.02110.4442-0.07520.0384-21.962-4.99922.831
124.215-2.258-1.53081.60921.18110.93770.027-0.4057-0.4670.0967-0.0091-0.00620.2419-0.0383-0.01790.5085-0.02790.06780.7067-0.0780.40491.319-23.0090.489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999

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