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- PDB-4zxi: Crystal Structure of holo-AB3403 a four domain nonribosomal pepti... -

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Basic information

Entry
Database: PDB / ID: 4zxi
TitleCrystal Structure of holo-AB3403 a four domain nonribosomal peptide synthetase bound to AMP and Glycine
ComponentsTyrocidine synthetase 3
KeywordsBIOSYNTHETIC PROTEIN / Nonribosomal peptide synthetase / NRPS / Condensation / Adenylation / PCP / Thioesterase / phosphopantetheine
Function / homology
Function and homology information


amide biosynthetic process / organonitrogen compound biosynthetic process / secondary metabolite biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / catalytic activity / nucleotide binding
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site ...Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / 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
ADENOSINE MONOPHOSPHATE / GLYCINE / NICKEL (II) ION / 4'-PHOSPHOPANTETHEINE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE / Abbfa_003403 / :
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsDrake, E.J. / Miller, B.R. / Allen, C.L. / Gulick, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-068440 United States
US Army Medical Research and Materiel CommandW81XWH-11-2-0218 United States
CitationJournal: Nature / Year: 2016
Title: Structures of two distinct conformations of holo-non-ribosomal peptide synthetases.
Authors: Drake, E.J. / Miller, B.R. / Shi, C. / Tarrasch, J.T. / Sundlov, J.A. / Allen, C.L. / Skiniotis, G. / Aldrich, C.C. / Gulick, A.M.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 17, 2016Group: Refinement description
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrocidine synthetase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1217
Polymers147,6661
Non-polymers1,4556
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-35 kcal/mol
Surface area51230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.100, 116.100, 342.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tyrocidine synthetase 3


Mass: 147665.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain AB307-0294) (bacteria)
Strain: AB307-0294 / Gene: ABBFA_003403 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7H2D0, UniProt: A0A0X1KH98*PLUS

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Non-polymers , 7 types, 22 molecules

#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-XP4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 591.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H60O8P / Comment: DMPA, phospholipid*YM
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.9 Å3/Da / Density % sol: 68.48 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.75-0.95 M potassium citrate, 0.01-0.025 M glycine, 0.05 M BTP

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→45.03 Å / Num. obs: 52900 / % possible obs: 99.99 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.82
Reflection shellResolution: 2.9→3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.25 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PDB_EXTRACT3.15data extraction
SCALAdata scaling
PHENIXrefinement
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.9→45.03 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 2971 3 %Random Selection
Rwork0.1744 95973 --
obs0.1759 52895 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.73 Å2 / Biso mean: 53.6487 Å2 / Biso min: 17.09 Å2
Refinement stepCycle: final / Resolution: 2.9→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10077 0 91 16 10184
Biso mean--58.14 39.52 -
Num. residues----1314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910400
X-RAY DIFFRACTIONf_angle_d1.18114180
X-RAY DIFFRACTIONf_chiral_restr0.0451641
X-RAY DIFFRACTIONf_plane_restr0.0061828
X-RAY DIFFRACTIONf_dihedral_angle_d13.633759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9-2.94750.39621410.319545504691
2.9475-2.99840.34271510.295345784729
2.9984-3.05290.3111420.281846194761
3.0529-3.11160.29141180.270345644682
3.1116-3.17510.28061440.260845464690
3.1751-3.24410.30941420.242845784720
3.2441-3.31950.25641340.226945944728
3.3195-3.40250.28951590.206145564715
3.4025-3.49450.22041350.190645724707
3.4945-3.59730.24641430.175245484691
3.5973-3.71330.21921400.168845784718
3.7133-3.8460.21581390.15245634702
3.846-3.99990.20271450.138746034748
3.9999-4.18180.18621340.130845514685
4.1818-4.40210.16721420.120345804722
4.4021-4.67760.17021490.118145614710
4.6776-5.03830.14951420.122945804722
5.0383-5.54460.19551360.142845654701
5.5446-6.3450.24551400.169445764716
6.345-7.98670.22681500.177445464696
7.9867-45.03990.21571450.170445654710
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)
12.7684-0.1869-0.65671.78490.12722.5065-0.0473-0.1855-0.28780.14570.1717-0.10310.0880.113-0.120.2254-0.0259-0.09410.44760.01570.28484.6603-59.6363-10.7392
22.0271-0.5042-0.48841.26750.11820.939-0.01670.31730.63280.08040.0382-0.2263-0.24560.1295-0.02430.2712-0.0759-0.05930.5120.11030.4623-5.1633-37.0298-16.1697
31.39980.01722.43040.30740.28354.3288-0.14620.56020.3510.02130.0033-0.6226-0.60010.51520.15560.49940.05750.01890.87510.39981.1102-17.5815-22.7319-43.0715
42.2627-0.35421.11382.4829-1.03932.4777-0.0155-0.0097-0.2539-0.1439-0.0653-0.17610.15350.12070.06780.27270.04920.03560.39080.13940.3699-43.7546-30.4039-51.1487
54.1369-1.35290.8332.2248-1.12383.6535-0.0168-0.0574-0.05430.04170.0645-0.0433-0.2210.1489-0.06360.2123-0.01280.03220.44020.10250.4051-39.577-42.8419-23.9892
61.0143-1.47372.87952.1268-4.17118.1364-0.55320.13170.45850.4969-0.5621-0.8862-1.07570.54691.10210.3442-0.0739-0.07820.38370.09330.5645-44.0175-47.8393-6.0158
74.10432.2349-0.72511.27480.05482.86490.04650.0121-0.25780.0108-0.0545-0.27060.1520.2918-0.0390.22360.03640.00170.27170.07580.3557-29.3077-58.9779-1.2317
80.57070.6153-1.58880.8631-2.10825.20410.260.4876-0.194-1.1479-0.2834-0.17270.2030.49920.02780.69110.07030.08310.5095-0.16710.6594-30.8739-73.683-0.9092
92.76370.5202-0.02942.4934-0.0742.44030.1252-0.1086-0.17220.2665-0.0835-0.12960.27290.0719-0.03140.3136-0.0211-0.01790.1590.04790.2284-45.6059-71.590113.8926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:190))A1054 - 1318
2X-RAY DIFFRACTION2chain 'A' and ((resseq 191:445))A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 446:480))A0
4X-RAY DIFFRACTION4chain 'A' and ((resseq 481:862))A0
5X-RAY DIFFRACTION5chain 'A' and ((resseq 863:959))A0
6X-RAY DIFFRACTION6chain 'A' and ((resseq 960:973))A0
7X-RAY DIFFRACTION7chain 'A' and ((resseq 974:1044))A0
8X-RAY DIFFRACTION8chain 'A' and ((resseq 1045:1053))A0
9X-RAY DIFFRACTION9chain 'A' and ((resseq 1054:1318))A0

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