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- PDB-5eks: Structure of 3-dehydroquinate synthase from Acinetobacter baumann... -

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Basic information

Entry
Database: PDB / ID: 5eks
TitleStructure of 3-dehydroquinate synthase from Acinetobacter baumannii in complex with NAD
Components3-dehydroquinate synthase
KeywordsLYASE / SSGCID / Acinetobacter baumannii / 3-dehydroquinate synthase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
3-dehydroquinate synthase family / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...3-dehydroquinate synthase family / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-dehydroquinate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of 3-dehydroquinate synthase from Acinetobacter baumannii in complex with NAD
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate synthase
B: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5046
Polymers81,1292
Non-polymers1,3754
Water11,205622
1
A: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2523
Polymers40,5641
Non-polymers6882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2523
Polymers40,5641
Non-polymers6882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 3-dehydroquinate synthase
hetero molecules

B: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5046
Polymers81,1292
Non-polymers1,3754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4780 Å2
ΔGint-40 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.400, 58.920, 104.810
Angle α, β, γ (deg.)90.000, 97.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-dehydroquinate synthase /


Mass: 40564.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB5075-UW
Gene: aroB, AB895_1177, AB988_0958, AB994_2838, ABCIP7010_3378, ABUW_0296, ACX61_01585, IOMTU433_0312, RU84_01465, TE32_01480, VM83_15710
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V5V8R5, 3-dehydroquinate synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.21 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents JCSG+ screen, B10: 50% PEG 200, 200mM MgCl2, 100mM Na-cacodylate/HCl pH 6.5; AcbaC.17683.a.B1.PS02371 at 10.6mg/ml, 2.5mM NAD; cryo: direct; tray 263095b10, puck jtp5-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 24, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 60565 / Num. obs: 60449 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.17 % / Biso Wilson estimate: 18.18 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.092 / Χ2: 0.976 / Net I/σ(I): 13.32 / Num. measured all: 252073
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.85-1.94.190.8580.5382.6218710447044630.61699.8
1.9-1.950.8870.4353.2618037431643150.498100
1.95-2.010.9220.354.0617660421142120.4100
2.01-2.070.940.2755.1817229409640980.315100
2.07-2.140.9630.236.2116658397739680.26499.8
2.14-2.210.9750.1847.5216093384238380.21199.9
2.21-2.290.980.1658.515588372937270.18999.9
2.29-2.390.9860.13510.0915040358335780.15599.9
2.39-2.490.9890.12111.0614262340633980.13899.8
2.49-2.620.9910.10213.0913834330733050.11799.9
2.62-2.760.9930.08715.1413155313931380.1100
2.76-2.930.9940.07517.3812368297629690.08699.8
2.93-3.130.9960.0620.5711456275727530.06999.9
3.13-3.380.9970.04924.3410717259825910.05799.7
3.38-3.70.9980.04427.739785239923850.0599.4
3.7-4.140.9980.03631.798918218021760.04199.8
4.14-4.780.9980.03433.537842192219100.03999.4
4.78-5.850.9980.03232.246837165216450.03799.6
5.85-8.270.9990.0332.655224127412710.03499.8
8.27-500.9980.02737.0626607317090.03197

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
Cootmodel building
PHENIXdev_2210refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3okf

3okf


Resolution: 1.85→48.029 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 2009 3.32 %Random selection
Rwork0.1671 58415 --
obs0.1686 60424 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.01 Å2 / Biso mean: 23.9529 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 1.85→48.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5346 0 90 624 6060
Biso mean--16.97 33.8 -
Num. residues----709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065632
X-RAY DIFFRACTIONf_angle_d0.8327688
X-RAY DIFFRACTIONf_chiral_restr0.05897
X-RAY DIFFRACTIONf_plane_restr0.005988
X-RAY DIFFRACTIONf_dihedral_angle_d12.2873345
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 (%)
1.85-1.89630.31581530.228541374290100
1.8963-1.94750.26281390.213141534292100
1.9475-2.00480.27281370.200341424279100
2.0048-2.06960.26241260.18941694295100
2.0696-2.14350.28131450.181641584303100
2.1435-2.22940.22951380.171741574295100
2.2294-2.33080.2451430.170241604303100
2.3308-2.45370.23111430.169741754318100
2.4537-2.60740.21481270.169741524279100
2.6074-2.80870.20711510.172141804331100
2.8087-3.09130.22561600.171241924352100
3.0913-3.53850.18081490.157641554304100
3.5385-4.45770.18041470.135942014348100
4.4577-48.0450.1821510.15664284443599
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)
11.62130.80.12941.6665-0.28153.24150.1624-0.17410.03740.3498-0.0412-0.0702-0.21920.1353-0.05470.2430.03440.02820.1448-0.02860.1722.729311.9595-10.4314
21.15740.2127-0.18651.1323-0.12831.02990.03230.00240.05740.17050.03790.0643-0.0877-0.0218-0.07540.14720.03140.02120.127-0.0030.139820.74676.3344-21.3788
31.04960.33590.21172.8151-0.36590.77350.0640.0307-0.00390.1113-0.04420.0463-0.02060.0325-0.03250.16620.02430.03540.16570.00410.116910.6393-12.5535-6.3974
45.40370.18260.00675.33012.06793.17160.0720.3874-0.23970.18320.1388-0.23150.17160.1894-0.18270.23230.05950.0040.13840.03920.094914.5705-25.8521-7.8091
53.01390.43660.61341.9714-0.60151.461-0.0423-0.233-0.35770.2035-0.0007-0.27330.03180.14290.04220.14860.045-0.00010.1230.00580.1689-8.5202-14.9906-32.47
61.2478-0.0073-0.41451.22920.04390.8953-0.0422-0.0114-0.02290.06080.06230.06070.0465-0.0256-0.01650.12270.0135-0.00270.1361-0.0060.1363-18.8796-8.7454-36.4829
70.82710.18590.32652.4102-0.32760.54380.0098-0.03690.02220.05730.0166-0.04140.0014-0.0353-0.02520.08880.0134-0.01020.1354-0.00830.117-0.56688.507-42.2202
82.3256-1.55850.39363.81080.54432.1561-0.0982-0.10660.21710.0957-0.01620.0764-0.2293-0.24590.12790.0907-0.0081-0.00170.1492-0.02240.1761-6.680422.1205-42.5654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 44 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 173 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 319 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 320 through 360 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 43 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 173 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 174 through 299 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 300 through 360 )B0

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