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Basic information

Entry
Database: PDB / ID: 5t0w
TitleCrystal structure of the ancestral amino acid-binding protein AncCDT-1, a precursor of cyclohexadienyl dehydratase
ComponentsAncCDT-1
KeywordsTRANSPORT PROTEIN / solute-binding protein / periplasmic binding protein / transport / amino acid
Function / homologyARGININE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsClifton, B.E. / Carr, P.D. / Jackson, C.J.
CitationJournal: To Be Published
Title: To be published
Authors: Clifton, B.E. / Kaczmarski, J.A. / Carr, P.D. / Jackson, C.J.
History
DepositionAug 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: AncCDT-1
B: AncCDT-1
C: AncCDT-1
D: AncCDT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8208
Polymers111,1194
Non-polymers7014
Water37821
1
A: AncCDT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9552
Polymers27,7801
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AncCDT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9552
Polymers27,7801
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: AncCDT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9552
Polymers27,7801
Non-polymers1751
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: AncCDT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9552
Polymers27,7801
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.030, 68.880, 318.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 14 - 246 / Label seq-ID: 14 - 246

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6
DetailsMonomer confirmed by size-exclusion chromatography

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Components

#1: Protein
AncCDT-1


Mass: 27779.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pDOTS7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: A crystal grown in a hanging drop of 2 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM arginine) + 2 uL precipitant (0.2 M lithium sulfate, 0.1 M TRIS pH 8.2, 22% (w/v) PEG 3350) ...Details: A crystal grown in a hanging drop of 2 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM arginine) + 2 uL precipitant (0.2 M lithium sulfate, 0.1 M TRIS pH 8.2, 22% (w/v) PEG 3350) was improved by three rounds of serial microseeding; the crystals were crushed and serially diluted in the precipitant, and new hanging drops were prepared by mixing 2 uL protein and 2 uL microseed suspension.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9501 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9501 Å / Relative weight: 1
ReflectionResolution: 2.59→33.66 Å / Num. obs: 33106 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.158 / Net I/σ(I): 8.2
Reflection shellResolution: 2.59→2.71 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.755 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLM1.0.7data reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZV2

4zv2


Resolution: 2.59→33.19 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.863 / SU B: 31.219 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 0.971 / ESU R Free: 0.359 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28733 1686 5.1 %RANDOM
Rwork0.25348 ---
obs0.25518 31387 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.419 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å2-0 Å2-0 Å2
2--0.55 Å20 Å2
3----2.9 Å2
Refinement stepCycle: LAST / Resolution: 2.59→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 0 48 21 7006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027133
X-RAY DIFFRACTIONr_bond_other_d0.0060.026702
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9589687
X-RAY DIFFRACTIONr_angle_other_deg1.195315392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91124.966298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.623151151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6991526
X-RAY DIFFRACTIONr_chiral_restr0.0770.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218063
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021551
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_it1.0451.643644
X-RAY DIFFRACTIONr_mcbond_other1.0461.643643
X-RAY DIFFRACTIONr_mcangle_it1.862.4514531
X-RAY DIFFRACTIONr_mcangle_other1.8592.4514532
X-RAY DIFFRACTIONr_scbond_it0.8361.6713489
X-RAY DIFFRACTIONr_scbond_other0.8361.6713489
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.52.4885156
X-RAY DIFFRACTIONr_long_range_B_refined3.10612.9348033
X-RAY DIFFRACTIONr_long_range_B_other3.10312.9338033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A125320.11
12B125320.11
21A120310.11
22C120310.11
31A122370.11
32D122370.11
41B123290.09
42C123290.09
51B125590.1
52D125590.1
61C122120.08
62D122120.08
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 128 -
Rwork0.348 2254 -
obs--98.59 %
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)
11.2674-0.06540.28813.2775-0.98162.0225-0.06160.09980.0991-0.33250.0704-0.03120.3444-0.1992-0.00880.2094-0.0267-0.02080.2622-0.02220.2346-9.82054.0655-6.6871
22.7257-2.1284-0.333511.4797-1.65571.27420.25350.17150.13620.2029-0.0177-0.0233-0.4136-0.1181-0.23580.2015-0.0162-0.00640.26730.05730.2562-14.716625.6374-15.512
34.605-1.53281.29922.0267-2.87074.28940.14190.1562-0.4493-0.5036-0.090.08290.76250.0415-0.05190.20520.0094-0.07550.2256-0.11310.2647-9.395714.9908-21.6344
41.39290.9018-0.19512.0913-1.10432.542-0.13140.23630.1773-0.07880.0411-0.2087-0.0482-0.00080.09030.13820.03370.02160.2415-0.00990.2793-1.61856.8641-1.6557
53.51110.7703-2.30192.2613-0.68554.28830.2076-0.25290.1438-0.215-0.02490.023-0.20970.143-0.18260.2055-0.0128-0.06790.2117-0.04120.1478-36.105336.8769-73.8163
69.15560.9314-1.32121.0587-1.99467.084-0.0911-0.3331-0.3987-0.1490.18040.55320.1366-0.9906-0.08930.03670.0459-0.11860.3947-0.01520.687-58.846337.5758-61.7279
71.4302-1.2721-2.6326.87441.82825.2507-0.0191-0.1018-0.13380.0236-0.0353-0.08840.1323-0.11610.05440.1226-0.0465-0.12190.37630.0780.2703-48.08432.5284-57.3263
83.2057-0.144-2.14433.7134-0.15593.5747-0.0893-0.0519-0.1991-0.44570.03930.12390.4012-0.39130.05010.3091-0.0349-0.09510.2582-0.00680.1672-37.584428.4126-80.4919
92.8077-0.70962.01744.4953.09165.6879-0.21080.15870.0126-0.54650.6316-0.53680.11870.8514-0.42080.61480.01120.03120.1617-0.09020.1422-9.12385.2359-45.3885
104.2171.34483.68863.05764.34747.0779-0.07770.0061-0.23490.324-0.09720.20150.3246-0.19990.17490.6001-0.0436-0.01670.0838-0.02190.0638-21.7664-3.8516-45.5844
117.69974.3859-0.17925.93973.71768.07430.10160.6750.18720.6894-0.20610.57260.6403-0.6350.10460.6843-0.11890.03340.16-0.06050.1282-28.3989-13.8379-58.1054
121.50730.28321.1462.10663.46896.0539-0.2053-0.13460.22140.1594-0.19470.1880.2713-0.39960.40.5578-0.0611-0.05890.09320.00550.1453-23.31892.374-48.0627
132.05710.17771.81042.94330.67234.68410.19880.1261-0.1431-0.1029-0.1825-0.0038-0.0773-0.1647-0.01630.17510.002-0.01750.2480.02430.2136-32.998736.3928-34.5683
140.02250.4271-0.066220.3715-3.94450.80670.0279-0.07210.04970.1128-0.2416-0.2722-0.06260.00090.21370.2581-0.1592-0.17720.6315-0.11350.5917-16.057458.5738-16.913
152.0069-0.82092.13043.8371-0.21568.2883-0.15470.28120.37760.0259-0.3752-0.4222-0.59890.95350.52990.23-0.0967-0.04820.19650.14510.2409-20.43645.8184-19.6091
162.84490.00531.10373.45881.58474.7756-0.0550.14380.1825-0.3185-0.26460.193-0.6904-0.37290.31950.25480.1077-0.03090.24410.03750.137-37.269145.3331-36.6987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 125
2X-RAY DIFFRACTION2A126 - 158
3X-RAY DIFFRACTION3A159 - 195
4X-RAY DIFFRACTION4A196 - 246
5X-RAY DIFFRACTION5B14 - 119
6X-RAY DIFFRACTION6B120 - 159
7X-RAY DIFFRACTION7B160 - 201
8X-RAY DIFFRACTION8B204 - 246
9X-RAY DIFFRACTION9C14 - 83
10X-RAY DIFFRACTION10C84 - 118
11X-RAY DIFFRACTION11C119 - 163
12X-RAY DIFFRACTION12C164 - 246
13X-RAY DIFFRACTION13D13 - 118
14X-RAY DIFFRACTION14D119 - 133
15X-RAY DIFFRACTION15D134 - 186
16X-RAY DIFFRACTION16D187 - 246

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