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- PDB-4dxe: 2.52 Angstrom resolution crystal structure of the acyl-carrier-pr... -

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Basic information

Entry
Database: PDB / ID: 4dxe
Title2.52 Angstrom resolution crystal structure of the acyl-carrier-protein synthase (AcpS)-acyl carrier protein (ACP) protein-protein complex from Staphylococcus aureus subsp. aureus COL
Components
  • Acyl carrier protein
  • acyl-carrier-protein synthase
KeywordsTRANSFERASE / acyl-carrier-protein synthase / acyl carrier protein / type II fatty acid synthesis pathway / Center for Structural Genomics of Infectious Diseases (CSGID)
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / lipid A biosynthetic process / acyl binding / acyl carrier activity / fatty acid biosynthetic process / magnesium ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. ...4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Holo-[acyl-carrier-protein] synthase / Acyl carrier protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsHalavaty, A.S. / Minasov, G. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.52 Angstrom resolution crystal structure of the acyl-carrier-protein synthase (AcpS)-acyl carrier protein (ACP) protein-protein complex from Staphylococcus aureus subsp. aureus COL
Authors: Halavaty, A.S. / Minasov, G. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acyl-carrier-protein synthase
B: acyl-carrier-protein synthase
C: acyl-carrier-protein synthase
D: acyl-carrier-protein synthase
E: acyl-carrier-protein synthase
F: acyl-carrier-protein synthase
H: Acyl carrier protein
L: Acyl carrier protein
K: Acyl carrier protein
G: Acyl carrier protein
J: Acyl carrier protein
I: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,44516
Polymers166,03712
Non-polymers4084
Water2,342130
1
A: acyl-carrier-protein synthase
B: acyl-carrier-protein synthase
C: acyl-carrier-protein synthase
H: Acyl carrier protein
L: Acyl carrier protein
K: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3259
Polymers83,0186
Non-polymers3063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: acyl-carrier-protein synthase
E: acyl-carrier-protein synthase
F: acyl-carrier-protein synthase
G: Acyl carrier protein
J: Acyl carrier protein
I: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1217
Polymers83,0186
Non-polymers1021
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.968, 102.961, 77.298
Angle α, β, γ (deg.)90.00, 115.87, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE ACPS-ACP COMPLEX IS FORMED BY TRIMERIC ACPS ENZYME THAT BINDS THREE ACP PROTEINS

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Components

#1: Protein
acyl-carrier-protein synthase / Holo-ACP synthase / 4'-phosphopantetheinyl transferase AcpS


Mass: 16371.500 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Staphylococcus aureus subsp. aureus COL / Gene: acpS, SACOL2061 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic
References: UniProt: Q5HED0, holo-[acyl-carrier-protein] synthase
#2: Protein
Acyl carrier protein / ACP


Mass: 11301.322 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Staphylococcus aureus subsp. aureus COL / Gene: acpP, apcP, SACOL1247 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic / References: UniProt: Q5HGK0
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: AcpS:ACP 1:1 molar ratio (0.33:0.33 mM) in 10 mM Tris-HCl pH 8.3, 0.5 M NaCl, 5 mM BME. The PACT suite B2 (#14: 0.1 M MIB buffer pH 5.0, 25 %(w/v) PEG1500), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2012 / Details: mirror
RadiationMonochromator: Si(111)Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.829
11L, -K, H20.171
ReflectionResolution: 2.51→30 Å / Num. all: 36820 / Num. obs: 36820 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.34
Reflection shellResolution: 2.51→2.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.43 / Num. unique all: 1863 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F09 (AcpS), 1F80 (ACP)

3f09
PDB Unreleased entry

1f80


Resolution: 2.51→28.82 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 26.111 / SU ML: 0.244 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25449 1865 5.1 %RANDOM
Rwork0.19971 ---
obs0.20257 34837 98.53 %-
all-34837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.391 Å2
Baniso -1Baniso -2Baniso -3
1--5.15 Å20 Å2-16.9 Å2
2---37.84 Å2-0 Å2
3---42.99 Å2
Refinement stepCycle: LAST / Resolution: 2.51→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8966 0 28 130 9124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229277
X-RAY DIFFRACTIONr_bond_other_d0.0010.026187
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.95712490
X-RAY DIFFRACTIONr_angle_other_deg0.698315226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.66151144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.89126.087483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.159151725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0141531
X-RAY DIFFRACTIONr_chiral_restr0.0710.21397
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021749
X-RAY DIFFRACTIONr_mcbond_it0.6331.55690
X-RAY DIFFRACTIONr_mcbond_other0.1341.52324
X-RAY DIFFRACTIONr_mcangle_it1.1829182
X-RAY DIFFRACTIONr_scbond_it2.03333587
X-RAY DIFFRACTIONr_scangle_it3.3474.53308
LS refinement shellResolution: 2.51→2.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 109 -
Rwork0.224 2066 -
obs-2066 79.58 %
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)
11.8251.2931-0.13554.3588-0.91511.6461-0.05790.0175-0.30460.01490.0894-0.06350.1418-0.2055-0.03150.02350.00210.01550.17040.00170.05762.275731.620415.3953
24.70810.69980.66954.5351-0.63532.01810.1505-0.21230.46090.2002-0.1601-0.1464-0.23290.04550.00960.06980.01350.02790.1813-0.03520.10985.034645.205115.1915
31.2128-0.20220.090312.10551.23834.5509-0.1062-0.0290.14640.3042-0.2292-0.0842-0.0331-0.05470.33530.0329-0.01730.04790.2440.05360.20712.367737.795611.9556
43.056-1.467-1.13161.75210.56251.75380.0070.31340.0492-0.314-0.0031-0.22750.17890.0832-0.00380.122-0.01040.10240.31570.06280.149824.713230.8484-4.5331
5-0.5129-0.6569-0.7284.90352.34275.9380.06490.11980.0206-0.2340.02570.0938-0.318-0.3608-0.09060.1296-0.00370.05250.36770.14750.208620.610439.1698-3.1966
60.52391.4894-0.77798.7982-0.46762.73510.03230.03390.1046-0.20370.087-0.3532-0.23130.008-0.11920.08530.00260.06020.25830.06510.206322.633842.80883.5603
72.28150.02530.55372.0591-0.7292.99080.0688-0.0112-0.029-0.02590.11020.20710.23190.0768-0.1790.0442-0.01380.04240.17380.01380.106530.312731.702624.8749
87.0936-0.20870.18814.0178-1.54019.208-0.2737-0.1970.37280.05130.0668-0.1974-0.17560.06460.2070.099-0.0364-0.00580.11240.05130.174228.098643.124523.1631
92.9902-2.62441.44042.7704-0.15892.9393-0.08730.09220.2289-0.1262-0.04710.0648-0.21260.35280.13440.08860.0141-0.01170.30410.01360.244824.293843.060418.5335
102.8129-1.3992-1.25585.07221.03231.39070.04520.05620.1282-0.11170.1039-0.41040.057-0.1305-0.14910.0266-0.00820.0060.2081-0.00840.033510.9515-0.420916.8562
112.79762.61331.32397.5258-0.47135.6442-0.0505-0.3805-0.22980.1471-0.0255-0.0657-0.0552-0.05750.0760.09030.0270.09830.2862-0.04330.14676.20853.93131.7076
121.4909-0.0019-0.53643.11570.31073.19760.0734-0.1183-0.04270.1177-0.2547-0.06660.1646-0.08840.18120.0531-0.02640.06430.2208-0.00970.096312.5074-6.518622.6437
133.08811.34270.06485.3910.60771.30730.07560.07310.02270.10020.0517-0.5837-0.14260.1811-0.12730.12620.00110.07130.23260.00070.103636.32092.08217.9918
143.44081.3418-0.53554.09870.12281.51940.12570.032-0.1397-0.1965-0.0904-0.33850.01450.2113-0.03530.0570.05130.06490.2203-0.01660.123735.5998-2.738613.1892
153.31141.2678-0.2070.80661.15233.31270.0658-0.0439-0.3205-0.01150.0308-0.11730.05790.3239-0.09660.08430.02350.0260.2937-0.06540.137828.6302-8.344714.0465
162.3833-0.29690.97612.1228-0.79242.4854-0.08780.05580.1538-0.01410.0223-0.0912-0.1222-0.02120.06550.0650.01730.06140.2006-0.01190.074314.42621.0994-2.9216
174.34232.6866.1515.45313.64517.33950.580.1962-0.1286-0.2-0.3978-0.19320.8220.2816-0.18220.30370.07070.07120.30640.04930.105517.5379-9.368-2.7798
182.4277-2.6386-0.558213.4704-3.47682.212-0.01370.1304-0.0979-0.16720.14050.25070.23680.0238-0.12680.0762-0.0265-0.00730.253-0.04680.096916.6731-8.69524.7909
1914.78686.27534.05839.54750.86046.32380.3124-0.1247-0.55760.1090.2018-0.37450.16950.3641-0.51420.09380.05980.09180.2616-0.01570.166949.56719.132510.5215
204.9478-1.9516-0.05632.55082.133612.2121-0.0542-0.0557-0.0925-0.21480.0513-0.047-0.3049-0.05080.00290.1113-0.02640.14250.22150.03150.195742.77226.414410.6556
217.5545-2.47882.27980.94111.159.09340.0923-0.60271.1201-0.36670.2169-0.3175-1.3571-0.1046-0.30920.4399-0.05890.06570.3672-0.01390.654150.574232.209215.2519
22-2.5177-0.698211.84713.0129-8.024435.8965-0.04420.13710.38-2.2684-0.39430.89651.6806-0.24150.43851.1638-0.0089-0.18091.21770.00950.6520.058819.7346-18.1463
234.93463.10751.04782.51870.77866.34680.0960.2922-0.1255-0.321-0.0187-0.1050.1160.1285-0.07730.19780.10660.00060.26960.04440.21835.945723.2227-7.8898
2413.2101-1.3560.3607-0.2847-0.59586.0692-0.18580.4361.15230.0518-0.0113-0.0068-1.15660.38840.19710.5565-0.041-0.01750.51680.17610.47526.129231.3451-16.048
254.1066-0.2376-0.43413.779-0.29616.3075-0.0743-0.20360.09470.3184-0.11720.1952-0.073-0.0990.19150.0536-0.03420.04280.134-0.03790.05478.040123.204436.5566
268.73020.5785.34215.488-0.555613.4131-0.0297-0.33120.6884-0.0748-0.02770.2258-0.0971-1.38050.05730.21650.05010.10020.39880.00230.2456-3.916329.935733.9681
277.00954.4788-3.5352.27542.16996.11141.56020.42321.37350.2312-0.44540.4559-1.7547-1.0619-1.11470.78830.11930.26340.5540.0630.58343.722732.760239.8426
2815.1106-3.85727.19727.0723-8.252811.8786-0.606-0.44920.9720.3175-0.0805-0.8110.17830.66770.68650.4120.1098-0.08510.4826-0.06890.329334.615815.31339.1903
2910.1654-1.2816-1.04254.98622.60267.3104-0.0655-0.1215-0.37780.26790.0901-0.20170.03890.3727-0.02470.1836-0.02420.03440.16740.05410.052533.80178.069733.6671
305.8061-7.144-1.57246.7521-1.73410.5227-0.2564-0.0634-0.54550.1383-0.02760.08220.61530.11110.2840.75980.0381-0.02250.5147-0.08840.621636.51750.822837.3984
3111.7433.5681.067112.614-0.38192.07210.0461-0.39550.33010.02820.05990.8335-0.3376-0.2968-0.10610.05970.0410.00960.2027-0.06040.1109-10.447614.495611.7002
324.3652-0.7070.81253.5677-0.26547.63470.1047-0.19970.1211-0.2218-0.10590.10070.1513-0.00750.00120.0674-0.04980.03810.1216-0.03270.1012-5.44617.118813.7859
330.87031.24792.56245.04111.24033.05390.4182-0.3798-0.41110.2450.0440.30371.0085-0.6549-0.46220.5689-0.06170.11360.4852-0.01970.4623-11.30830.072616.3045
344.2972-2.2085-1.28510.8827-0.018920.39210.23160.28370.5579-0.4374-0.0335-0.1501-1.11740.2185-0.19810.6082-0.03420.03360.49460.05790.381734.688714.2421-16.8779
358.24941.83322.2842.1637-1.17145.77530.13850.0731-0.15510.1250.0738-0.27580.10170.0268-0.21230.16220.07180.13460.25890.02310.258332.58289.0813-7.2764
3614.65670.70912.10221.39963.05684.54990.38440.6763-0.45710.3087-0.0191-0.3141.04910.0168-0.36520.67170.05810.18930.398-0.05380.408930.75571.9088-16.7786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 58
2X-RAY DIFFRACTION2A59 - 99
3X-RAY DIFFRACTION3A100 - 117
4X-RAY DIFFRACTION4B0 - 49
5X-RAY DIFFRACTION5B50 - 83
6X-RAY DIFFRACTION6B87 - 117
7X-RAY DIFFRACTION7C0 - 58
8X-RAY DIFFRACTION8C59 - 90
9X-RAY DIFFRACTION9C91 - 118
10X-RAY DIFFRACTION10D-1 - 19
11X-RAY DIFFRACTION11D20 - 45
12X-RAY DIFFRACTION12D46 - 117
13X-RAY DIFFRACTION13E0 - 38
14X-RAY DIFFRACTION14E39 - 89
15X-RAY DIFFRACTION15E90 - 117
16X-RAY DIFFRACTION16F-1 - 63
17X-RAY DIFFRACTION17F64 - 90
18X-RAY DIFFRACTION18F91 - 117
19X-RAY DIFFRACTION19G0 - 20
20X-RAY DIFFRACTION20G21 - 48
21X-RAY DIFFRACTION21G49 - 75
22X-RAY DIFFRACTION22H0 - 9
23X-RAY DIFFRACTION23H10 - 48
24X-RAY DIFFRACTION24H49 - 73
25X-RAY DIFFRACTION25I-1 - 44
26X-RAY DIFFRACTION26I45 - 58
27X-RAY DIFFRACTION27I59 - 75
28X-RAY DIFFRACTION28J-1 - 20
29X-RAY DIFFRACTION29J21 - 54
30X-RAY DIFFRACTION30J55 - 74
31X-RAY DIFFRACTION31K0 - 21
32X-RAY DIFFRACTION32K22 - 51
33X-RAY DIFFRACTION33K52 - 75
34X-RAY DIFFRACTION34L-1 - 14
35X-RAY DIFFRACTION35L15 - 47
36X-RAY DIFFRACTION36L48 - 74

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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