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

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Basic information

Entry
Database: PDB / ID: 4zxh
TitleCrystal Structure of holo-AB3403 a four domain nonribosomal peptide synthetase from Acinetobacter Baumanii
ComponentsABBFA_003403
KeywordsBIOSYNTHETIC PROTEIN / Nonribosomal peptide synthetase / NRPS / Condensation / Adenylation / PCP / Thioesterase / phosphopantetheine
Function / homology
Function and homology information


amide biosynthetic process / secondary metabolite biosynthetic process / organonitrogen compound 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
: / NICKEL (II) ION / 4'-PHOSPHOPANTETHEINE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Abbfa_003403 / :
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.7 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)GM068440 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

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Assembly

Deposited unit
A: ABBFA_003403
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,8015
Polymers147,6661
Non-polymers1,1354
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-31 kcal/mol
Surface area53000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.187, 116.187, 348.607
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 ABBFA_003403


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 , 5 types, 29 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-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.98 Å3/Da / Density % sol: 69.12 %
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: 0.9796 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.7→49.8 Å / Num. obs: 66559 / % possible obs: 99.96 % / Redundancy: 2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.91
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.49 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.795 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1999 3 %Random Selection
Rwork0.1789 64541 --
obs0.1806 66540 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.51 Å2 / Biso mean: 46.0095 Å2 / Biso min: 5.07 Å2
Refinement stepCycle: final / Resolution: 2.7→49.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10189 0 75 25 10289
Biso mean--55.84 29.33 -
Num. residues----1314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910495
X-RAY DIFFRACTIONf_angle_d1.17814293
X-RAY DIFFRACTIONf_chiral_restr0.0451638
X-RAY DIFFRACTIONf_plane_restr0.0061852
X-RAY DIFFRACTIONf_dihedral_angle_d13.4613838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.76750.31361390.247945254664100
2.7675-2.84240.3421400.252745034643100
2.8424-2.9260.37681410.250345434684100
2.926-3.02040.27641400.233545394679100
3.0204-3.12840.29321410.223745514692100
3.1284-3.25360.28161410.220645304671100
3.2536-3.40160.26641420.215545934735100
3.4016-3.58090.23221410.18945814722100
3.5809-3.80520.23431420.168545654707100
3.8052-4.09890.21041440.149646254769100
4.0989-4.51110.19411430.138846264769100
4.5111-5.16330.15691440.1346634807100
5.1633-6.5030.23481470.161847444891100
6.503-49.80340.1961540.16094953510799
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)
12.6099-0.25630.31691.4559-0.10011.5443-0.0937-0.17510.25470.19760.15520.1531-0.2038-0.17520.00030.1691-0.02450.07480.38350.03180.2388-4.292160.6443163.2479
21.3588-0.4603-2.30781.0678-0.20174.9480.03870.8336-0.56350.02660.01010.66820.4603-0.96330.9250.3659-0.0188-0.04040.7526-0.43970.770717.24923.3821131.2673
31.8936-0.3842-1.13412.00991.21652.39690.02460.11530.1872-0.235-0.10180.1271-0.2588-0.164-0.01080.22970.0472-0.03390.3437-0.10270.251743.668631.2616122.5092
44.583-1.2783-1.30351.31610.9513.71520.05420.08660.1411-0.01230.02590.06460.1234-0.1201-0.06270.1395-0.0564-0.01760.3489-0.08750.292139.726643.1514150.299
50.0918-0.3596-0.54421.37322.09553.2143-0.28890.2325-0.07330.1668-0.15620.23380.4959-0.36590.20050.1659-0.13650.00540.3471-0.12570.480544.285948.1308168.3005
64.83082.62910.33522.1636-0.57382.6722-0.07650.10020.1751-0.02630.025-0.0583-0.1177-0.20220.00750.13710.0479-0.00290.2255-0.05980.220229.702659.7317172.8109
70.15750.0787-0.53670.2726-0.06361.98950.0060.49-0.1997-0.84790.06390.284-0.0963-1.5781-0.10440.55460.001-0.1840.49020.06420.57331.784574.8607174.0367
82.32530.71660.37412.11410.14872.15610.0773-0.09940.26780.2893-0.04820.073-0.2764-0.09550.00810.2706-0.01840.01920.1014-0.03770.22646.017372.1765188.6479
92.3571-0.62850.4631.0471-0.2740.83810.01120.2265-0.73850.16470.02730.23730.312-0.0886-0.14420.1705-0.08240.03450.4336-0.06730.41855.396337.6331158.0315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:190))A191 - 445
2X-RAY DIFFRACTION2chain 'A' and ((resseq 446:480))A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 481:862))A0
4X-RAY DIFFRACTION4chain 'A' and ((resseq 863:959))A0
5X-RAY DIFFRACTION5chain 'A' and ((resseq 960:973))A0
6X-RAY DIFFRACTION6chain 'A' and ((resseq 974:1044))A0
7X-RAY DIFFRACTION7chain 'A' and ((resseq 1045:1053))A0
8X-RAY DIFFRACTION8chain 'A' and ((resseq 1054:1318))A0
9X-RAY DIFFRACTION9chain 'A' and ((resseq 191:445))A0

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