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- PDB-7dq5: Crystal structure of HitB in complex with (S)-beta-phenylalanine ... -

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Basic information

Entry
Database: PDB / ID: 7dq5
TitleCrystal structure of HitB in complex with (S)-beta-phenylalanine sulfamoyladenosine
ComponentsPutative ATP-dependent b-aminoacyl-ACP synthetase
KeywordsLIGASE / Hitachimycin / Polyketide biosynthesis / ATP binding / Adenylation
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
AMP-binding / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Chem-8PZ / Putative ATP-dependent b-aminoacyl-ACP synthetase
Similarity search - Component
Biological speciesEmbleya scabrispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKudo, F. / Takahashi, S. / Miyanaga, A. / Nakazawa, Y. / Eguchi, T.
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Mutational Biosynthesis of Hitachimycin Analogs Controlled by the beta-Amino Acid-Selective Adenylation Enzyme HitB.
Authors: Kudo, F. / Takahashi, S. / Miyanaga, A. / Nakazawa, Y. / Nishino, K. / Hayakawa, Y. / Kawamura, K. / Ishikawa, F. / Tanabe, G. / Iwai, N. / Nagumo, Y. / Usui, T. / Eguchi, T.
History
DepositionDec 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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: Putative ATP-dependent b-aminoacyl-ACP synthetase
B: Putative ATP-dependent b-aminoacyl-ACP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4176
Polymers119,3492
Non-polymers1,0674
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-20 kcal/mol
Surface area37520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.681, 93.639, 165.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: _

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALAA9 - 47025 - 486
2THRTHRBB9 - 52725 - 543

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Components

#1: Protein Putative ATP-dependent b-aminoacyl-ACP synthetase


Mass: 59674.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Embleya scabrispora (bacteria) / Gene: hitB / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7R6G7
#2: Chemical ChemComp-8PZ / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-phenyl-propanoyl]sulfamate


Mass: 493.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 400, calcium acetate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 39398 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Net I/σ(I): 13.1
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 6 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4375 / CC1/2: 0.858 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M01

6m01


Resolution: 2.45→47.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 27.532 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.499 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 2002 5.1 %RANDOM
Rwork0.2102 ---
obs0.2128 37334 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.03 Å2 / Biso mean: 53.06 Å2 / Biso min: 22.32 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å20 Å20 Å2
2--5.92 Å20 Å2
3----3.13 Å2
Refinement stepCycle: final / Resolution: 2.45→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7135 0 70 111 7316
Biso mean--40.44 42.37 -
Num. residues----931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137362
X-RAY DIFFRACTIONr_bond_other_d0.0030.0177014
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.65110030
X-RAY DIFFRACTIONr_angle_other_deg1.2791.57316102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4215920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02618.998419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.573151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3511593
X-RAY DIFFRACTIONr_chiral_restr0.0740.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021692
Refine LS restraints NCS

Ens-ID: 1 / Number: 12423 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 143 -
Rwork0.312 2731 -
all-2874 -
obs--99.9 %
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)
10.2460.0778-0.01580.11180.10920.44080.003-0.0045-0.01480.0199-0.0112-0.00810.00940.06250.00810.02850.02470.00640.3642-0.00280.00515.928-23.477-13.677
20.38430.05-0.07840.6274-0.30020.7683-0.02110.10640.0381-0.1010.04330.10110.0087-0.0162-0.02220.03410.0057-0.02010.3571-0.01810.0238-13.2-23.834-50.262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 602
2X-RAY DIFFRACTION2B9 - 602

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