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- PDB-6ojd: A high-resolution crystal structure of covalent complex of NocB t... -

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Basic information

Entry
Database: PDB / ID: 6ojd
TitleA high-resolution crystal structure of covalent complex of NocB thioesterase domain with fluorophosphonate nocardicin G analog
ComponentsNocB
KeywordsHYDROLASE / Nonribosomal peptide synthetase (NRPS) / thioesterase / epimerization / alpha/beta hydrolase fold
Function / homology
Function and homology information


amide biosynthetic process / secondary metabolite biosynthetic process / organonitrogen compound biosynthetic process / carboxylic acid metabolic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / 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. ...Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / 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. / Chloramphenicol acetyltransferase-like domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-MUY / Phenyloxazoline synthase MbtB
Similarity search - Component
Biological speciesNocardia uniformis subsp. tsuyamanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPatel, K.D. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM116957 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions.
Authors: Patel, K.D. / d'Andrea, F.B. / Gaudelli, N.M. / Buller, A.R. / Townsend, C.A. / Gulick, A.M.
History
DepositionApr 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NocB
B: NocB
C: NocB
D: NocB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,91824
Polymers110,9764
Non-polymers2,94320
Water7,026390
1
A: NocB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6128
Polymers27,7441
Non-polymers8687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NocB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5727
Polymers27,7441
Non-polymers8286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NocB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4806
Polymers27,7441
Non-polymers7365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NocB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2553
Polymers27,7441
Non-polymers5112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.680, 78.560, 146.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NocB


Mass: 27743.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia uniformis subsp. tsuyamanensis (bacteria)
Gene: nocB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5J1Q6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MUY / (R)-[(S)-[(3S)-3-{[(2R)-2-amino-2-(4-hydroxyphenyl)acetyl]amino}-2-oxoazetidin-1-yl](4-hydroxyphenyl)methyl]methylphosphinic acid


Mass: 419.368 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H22N3O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 390 / 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: 1.92 Å3/Da / Density % sol: 35.91 % / Description: Thin plate-like crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 50mM CHES pH 9.0, 250mM CaCl2, 30% PEG 4K / PH range: 8.5-9.0

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Data collection

DiffractionMean temperature: 113.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03323 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.99→43.37 Å / Num. obs: 58017 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Χ2: 0.95 / Net I/σ(I): 9.8
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.626 / Num. unique obs: 4265 / CC1/2: 0.783 / Rpim(I) all: 0.402 / Rrim(I) all: 0.747 / Χ2: 0.86 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OJC

6ojc


Resolution: 1.99→41.553 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 23.13
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2001 3.46 %Random selection
Rwork0.1876 ---
obs0.1889 57905 97.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→41.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 188 393 7161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096917
X-RAY DIFFRACTIONf_angle_d0.9149479
X-RAY DIFFRACTIONf_dihedral_angle_d17.1924000
X-RAY DIFFRACTIONf_chiral_restr0.0561076
X-RAY DIFFRACTIONf_plane_restr0.0111256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.03980.36241460.29393960X-RAY DIFFRACTION98
2.0398-2.09490.27821390.25643944X-RAY DIFFRACTION98
2.0949-2.15660.26421530.2263978X-RAY DIFFRACTION99
2.1566-2.22620.22271320.20884004X-RAY DIFFRACTION99
2.2262-2.30580.27031530.2093959X-RAY DIFFRACTION98
2.3058-2.39810.2031390.18253997X-RAY DIFFRACTION99
2.3981-2.50720.22161460.16953979X-RAY DIFFRACTION98
2.5072-2.63940.20951490.16663997X-RAY DIFFRACTION98
2.6394-2.80470.23181400.17773981X-RAY DIFFRACTION98
2.8047-3.02120.22961360.16994003X-RAY DIFFRACTION98
3.0212-3.32510.21921400.17343970X-RAY DIFFRACTION97
3.3251-3.8060.18611490.16163971X-RAY DIFFRACTION96
3.806-4.7940.18561380.15684022X-RAY DIFFRACTION96
4.794-41.56230.25371410.22364139X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 19.4478 Å / Origin y: 28.7118 Å / Origin z: 22.3427 Å
111213212223313233
T0.1791 Å2-0.0084 Å20.0252 Å2-0.1647 Å20.0037 Å2--0.1801 Å2
L0.1136 °2-0.0675 °20.0258 °2-0.2918 °20.0282 °2--0.3765 °2
S0.0045 Å °0.0201 Å °-0.0052 Å °-0.0068 Å °-0.0047 Å °-0.0113 Å °-0.0163 Å °0.0019 Å °-0.0016 Å °
Refinement TLS groupSelection details: all

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