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- PDB-7tzp: Crystal Structure of Putataive Short-Chain Dehydrogenase/Reductas... -

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Basic information

Entry
Database: PDB / ID: 7tzp
TitleCrystal Structure of Putataive Short-Chain Dehydrogenase/Reductase (FabG) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 in Complex with NADH
Components3-oxoacyl-ACP reductase
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / FabG / NADH
Function / homology
Function and homology information


: / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 3-oxoacyl-ACP reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionFeb 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
C: 3-oxoacyl-ACP reductase
D: 3-oxoacyl-ACP reductase
E: 3-oxoacyl-ACP reductase
F: 3-oxoacyl-ACP reductase
G: 3-oxoacyl-ACP reductase
H: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,60960
Polymers209,9828
Non-polymers5,62752
Water12,556697
1
A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
C: 3-oxoacyl-ACP reductase
D: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,76330
Polymers104,9914
Non-polymers2,77226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17570 Å2
ΔGint-147 kcal/mol
Surface area32510 Å2
MethodPISA
2
E: 3-oxoacyl-ACP reductase
F: 3-oxoacyl-ACP reductase
hetero molecules

E: 3-oxoacyl-ACP reductase
F: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,53826
Polymers104,9914
Non-polymers2,54722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x-1/2,y,-z-1/21
Buried area16920 Å2
ΔGint-125 kcal/mol
Surface area32610 Å2
MethodPISA
3
G: 3-oxoacyl-ACP reductase
H: 3-oxoacyl-ACP reductase
hetero molecules

G: 3-oxoacyl-ACP reductase
H: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,15434
Polymers104,9914
Non-polymers3,16330
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+1/2,y,-z-1/21
Buried area17580 Å2
ΔGint-129 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.387, 256.020, 260.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11B-535-

HOH

21F-438-

HOH

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
3-oxoacyl-ACP reductase / 3-oxoacyl-ACP reductase FabG


Mass: 26247.744 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
Gene: fabG_6, DBX64_14690, SAMEA4364603_02057 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic
References: UniProt: A0A332H2K8, 3-oxoacyl-[acyl-carrier-protein] reductase

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Non-polymers , 6 types, 749 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 13.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: ComPAS (A2), 0.5M Potassium chloride, 12% (w/v) PEGr800, 10% (w/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2020 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 82427 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.061 / Rrim(I) all: 0.169 / Rsym value: 0.157 / Χ2: 1.163 / Net I/σ(I): 13.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 2 / Num. unique obs: 4121 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.475 / Rrim(I) all: 1.318 / Rsym value: 1.229 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 18.357 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.491 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 4266 5.2 %RANDOM
Rwork0.1892 ---
obs0.1911 78066 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.1 Å2 / Biso mean: 49.129 Å2 / Biso min: 5.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å2-0 Å20 Å2
2---0.57 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 2.6→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14369 0 344 700 15413
Biso mean--54.71 41.9 -
Num. residues----1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01314931
X-RAY DIFFRACTIONr_bond_other_d0.0350.01514586
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.63920158
X-RAY DIFFRACTIONr_angle_other_deg2.2261.5833358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.39551970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.65722.181697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.105152272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.51815106
X-RAY DIFFRACTIONr_chiral_restr0.0480.22052
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217285
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023379
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 281 -
Rwork0.285 5715 -
all-5996 -
obs--99.75 %
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)
13.3816-0.21550.79652.9283-0.96524.17950.11190.06340.34320.1542-0.03790.0449-0.3819-0.211-0.0740.26040.07120.14250.17160.06070.10579.18-37.673-26.667
22.2459-1.8608-1.76164.40231.9933.4350.19250.00770.2356-0.1653-0.0431-0.2548-0.06130.0936-0.14930.23840.01890.10320.34040.03870.090316.831-51.645-26.225
31.7147-0.8582-1.76331.3588-0.00873.70860.0841-0.11530.04060.0799-0.03820.0747-0.05580.06-0.04590.37620.02820.07950.37970.03290.16627.313-55.181-22.974
41.00460.6764-0.52982.64410.13316.03620.09780.27540.202-0.4072-0.08940.1907-0.364-0.1639-0.00840.22240.08530.04950.330.05890.06320.015-53.513-35.273
54.6324-1.4749-1.16631.7315-1.53944.60950.05650.0206-0.17480.15710.0535-0.00750.4120.0146-0.110.47020.03210.00790.4675-0.00740.239826.018-86.539-21.215
61.2503-1.0083-0.3244.08071.25170.92910.05890.00050.02530.0953-0.1103-0.2540.08970.11850.05130.48270.03550.06650.50720.04120.233526.911-72.25-25.346
71.22850.30191.244.23512.36095.83330.16890.15380.0258-0.1209-0.0089-0.13560.0420.0146-0.160.31880.0470.02320.39940.00880.100314.321-72.367-27.443
81.59080.2143-0.32661.7025-0.11057.07110.0755-0.1328-0.11110.2421-0.1177-0.0140.11150.33410.04210.1987-0.0084-00.2218-0.01230.010610.982-79.53-13.703
94.914-0.61781.0715.3951-0.40687.49710.1894-0.0767-0.2464-0.144-0.1103-0.11120.73510.4933-0.07910.4497-0.0111-0.12930.3241-0.13080.2326-1.388-98.055-27.207
101.7544-0.36260.08912.9453-0.56081.77810.21940.1278-0.5001-0.2705-0.020.57760.339-0.2327-0.19940.3834-0.0846-0.1680.4232-0.08410.3282-15.107-92.119-26.696
112.5385-0.7951.6351.8508-0.87873.89260.1934-0.1198-0.0508-0.0263-0.03890.35410.1298-0.222-0.15450.3338-0.0397-0.04030.3536-0.06930.1475-6.717-81.906-23.124
122.41770.11921.62852.2485-0.11348.60910.16750.2848-0.1183-0.5165-0.24290.33170.4444-0.16240.07530.22990.0583-0.08650.2683-0.09320.0670.451-83.294-35.507
134.3569-1.46060.01625.3653.56944.81260.1082-0.10660.36460.1157-0.11440.8247-0.6624-0.61470.00620.48010.11490.13750.5890.02550.5822-25.472-50.752-20.478
145.49841.14281.76529.07912.91354.64790.20240.15660.52150.3112-0.19040.9628-0.2486-0.6402-0.0120.07740.13360.09890.4080.06390.3831-30.41-56.952-26.943
151.3588-1.15630.26564.67-3.50174.87750.14550.08070.0883-0.1048-0.05870.6410.1026-0.1854-0.08670.2309-0.0535-0.02980.4338-0.00750.3161-22.596-72.422-22.627
161.36220.4247-0.93822.4544-0.31831.4570.1930.2150.0355-0.1899-0.01260.46330.0936-0.1775-0.18040.31690.04120.02550.4075-0.00410.2276-14.061-63.983-25.776
171.18610.31180.69131.3599-2.469310.51640.1401-0.0120.22910.2595-0.05560.3025-0.1419-0.3924-0.08440.2434-0.00170.1240.2729-0.00630.1207-9.823-57.593-13.912
181.85950.50860.0153.1583-0.32832.30170.0809-0.52950.39410.67-0.06920.1444-0.0239-0.0314-0.01170.4381-0.0558-0.14920.3902-0.19710.352-31.417-105.164-36.552
194.80514.7744-3.99710.5411-7.38618.51640.0308-0.23220.09880.4149-0.0998-0.5696-0.11880.29040.06910.2175-0.0603-0.17870.2493-0.10.3093-22.311-108.248-49.564
202.74681.6947-1.48362.9183-1.0272.990.1727-0.22340.14660.0471-0.1538-0.11210.10310.183-0.01890.3884-0.0336-0.1490.3597-0.10120.3608-33.648-110.211-52.142
2112.34443.07375.82268.3258-2.016112.9133-0.09210.66611.0433-0.22440.03460.0148-0.78871.53140.05750.4882-0.0798-0.00850.2133-0.12040.7897-35.598-85.69-51.36
222.4598-0.2430.47354.9612-0.67673.1828-0.0272-0.4980.44050.56710.05670.3025-0.2004-0.3233-0.02950.1924-0.0124-0.07840.2343-0.16530.3213-44.107-103.066-49.325
235.60962.2919-2.5934.67842.76525.8777-0.25240.3962-0.1688-0.67640.2547-0.5440.01340.5195-0.00240.59840.21330.18030.85590.11720.7063-13.982-111.411-82.209
242.7965-0.8702-0.52763.93110.58093.67460.07240.3890.2339-0.2307-0.1331-0.5560.03270.87330.06070.0395-0.01730.03590.50320.07090.416-9.033-104.681-75.87
252.53472.0097-1.491211.4906-7.03087.6327-0.13810.2030.1312-0.00610.0074-0.69950.13420.35790.13070.0651-0.0128-0.1160.1974-0.06660.3036-17.589-109.203-61.094
261.97350.28211.422.35890.22282.61660.17270.19270.2299-0.05210.0277-0.25060.21450.3605-0.20040.1580.0618-0.02150.1660.01870.178-27.862-112.402-72.423
275.99590.8714-1.93342.5756-0.17543.0631-0.11580.2109-0.1161-0.26690.1942-0.25080.08850.1222-0.07830.3083-0.049-0.02540.25890.0160.114836.65-95.061-97.478
281.8366-0.8719-0.84282.40221.39833.2641-0.09630.0445-0.1594-0.22950.17480.3167-0.0253-0.1925-0.07850.2954-0.0685-0.10070.33470.09330.195824.385-98.49-85.466
291.62-1.1344-1.02891.03370.08782.74390.0387-0.0288-0.1455-0.01740.06190.08370.267-0.1968-0.10060.3859-0.0453-0.07270.37580.06010.24434.265-100.304-78.978
301.63090.18230.00555.8497-0.6323.8098-0.0109-0.02190.2671-0.27770.37080.1211-0.5292-0.0322-0.360.161-0.061-0.00380.26250.03090.117241.568-87.823-80.007
313.7961-0.79621.19145.0906-1.8186.01370.0277-0.2533-0.28390.31570.35330.39830.1972-0.8232-0.3810.0701-0.0570.02650.45060.17850.123411.461-99.7-51.973
321.4555-1.6147-1.57949.05386.28076.4449-0.0817-0.2399-0.1612-0.05710.15050.41630.1625-0.2654-0.06890.1837-0.0523-0.06250.30990.12340.152917.848-101.571-70.933
330.62671.20090.28532.50641.04394.2052-0.04450.01580.0197-0.0910.22130.11960.0217-0.2589-0.17670.193-0.0082-0.02670.39780.10820.203225.522-96.895-61.544
342.1971-1.33040.61398.7303-1.66391.4384-0.0547-0.0859-0.292-0.46680.38390.43230.435-0.217-0.32930.2778-0.0769-0.07880.21880.04530.087329.598-109.362-54.768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 76
2X-RAY DIFFRACTION2A77 - 127
3X-RAY DIFFRACTION3A128 - 187
4X-RAY DIFFRACTION4A188 - 244
5X-RAY DIFFRACTION5B0 - 49
6X-RAY DIFFRACTION6B50 - 129
7X-RAY DIFFRACTION7B130 - 183
8X-RAY DIFFRACTION8B184 - 244
9X-RAY DIFFRACTION9C0 - 31
10X-RAY DIFFRACTION10C32 - 127
11X-RAY DIFFRACTION11C128 - 187
12X-RAY DIFFRACTION12C188 - 244
13X-RAY DIFFRACTION13D0 - 49
14X-RAY DIFFRACTION14D50 - 90
15X-RAY DIFFRACTION15D91 - 128
16X-RAY DIFFRACTION16D129 - 188
17X-RAY DIFFRACTION17D189 - 244
18X-RAY DIFFRACTION18E1 - 98
19X-RAY DIFFRACTION19E99 - 128
20X-RAY DIFFRACTION20E129 - 183
21X-RAY DIFFRACTION21E184 - 204
22X-RAY DIFFRACTION22E205 - 244
23X-RAY DIFFRACTION23F0 - 49
24X-RAY DIFFRACTION24F50 - 88
25X-RAY DIFFRACTION25F89 - 129
26X-RAY DIFFRACTION26F130 - 244
27X-RAY DIFFRACTION27G-2 - 60
28X-RAY DIFFRACTION28G61 - 127
29X-RAY DIFFRACTION29G128 - 187
30X-RAY DIFFRACTION30G188 - 244
31X-RAY DIFFRACTION31H-1 - 90
32X-RAY DIFFRACTION32H91 - 127
33X-RAY DIFFRACTION33H128 - 188
34X-RAY DIFFRACTION34H189 - 244

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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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