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- PDB-6xrs: Crystal structure of a GTP-binding protein EngA (Der homolog) fro... -

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Basic information

Entry
Database: PDB / ID: 6xrs
TitleCrystal structure of a GTP-binding protein EngA (Der homolog) from Neisseria gonorrhoeae bound to GDP
ComponentsGTPase Der
KeywordsHYDROLASE / GTPase / KH domain / National Institute of Allergy and Infectious Diseases / NIAID / STI / STD / conformational change / GTP-GDP sensing / double hydrolase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


ribosome biogenesis / GTP binding / ATP hydrolysis activity
Similarity search - Function
EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Small GTP-binding protein domain ...EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Small GTP-binding protein domain / K homology domain-like, alpha/beta / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / IODIDE ION / GTPase Der
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a GTP-binding protein EngA (Der homolog) from Neisseria gonorrhoeae bound to GDP
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase Der
B: GTPase Der
C: GTPase Der
D: GTPase Der
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,93819
Polymers202,5944
Non-polymers3,34415
Water1,946108
1
A: GTPase Der
C: GTPase Der
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,98710
Polymers101,2972
Non-polymers1,6908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-52 kcal/mol
Surface area33570 Å2
MethodPISA
2
B: GTPase Der
D: GTPase Der
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9519
Polymers101,2972
Non-polymers1,6547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-25 kcal/mol
Surface area33770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.160, 139.640, 127.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 16 through 17 and (name N...
21(chain B and ((resid 16 through 17 and (name N...
31(chain C and ((resid 16 through 17 and (name N...
41(chain D and ((resid 16 through 17 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 16 through 17 and (name N...A16 - 17
121(chain A and ((resid 16 through 17 and (name N...A15 - 601
131(chain A and ((resid 16 through 17 and (name N...A15 - 601
141(chain A and ((resid 16 through 17 and (name N...A15 - 601
151(chain A and ((resid 16 through 17 and (name N...A15 - 601
211(chain B and ((resid 16 through 17 and (name N...B16 - 17
221(chain B and ((resid 16 through 17 and (name N...B15 - 601
231(chain B and ((resid 16 through 17 and (name N...B15 - 601
241(chain B and ((resid 16 through 17 and (name N...B15 - 601
251(chain B and ((resid 16 through 17 and (name N...B15 - 601
311(chain C and ((resid 16 through 17 and (name N...C16 - 17
321(chain C and ((resid 16 through 17 and (name N...C16 - 501
331(chain C and ((resid 16 through 17 and (name N...C16 - 501
341(chain C and ((resid 16 through 17 and (name N...C16 - 501
351(chain C and ((resid 16 through 17 and (name N...C16 - 501
411(chain D and ((resid 16 through 17 and (name N...D16 - 17
421(chain D and ((resid 16 through 17 and (name N...D15 - 501
431(chain D and ((resid 16 through 17 and (name N...D15 - 501
441(chain D and ((resid 16 through 17 and (name N...D15 - 501
451(chain D and ((resid 16 through 17 and (name N...D15 - 501

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Components

#1: Protein
GTPase Der


Mass: 50648.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: der, engA, NGK_0592 / Production host: Escherichia coli (E. coli) / References: UniProt: B4RKD2*PLUS
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: NegoA.00852.a.D11.PD38388 CID102204 at 3.75 mg/mL against a focus screen based off Morpheus B10 6% PEG 8000, 20% ethylene glycol, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI, 0.1 M Bicine pH 8.6, ...Details: NegoA.00852.a.D11.PD38388 CID102204 at 3.75 mg/mL against a focus screen based off Morpheus B10 6% PEG 8000, 20% ethylene glycol, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI, 0.1 M Bicine pH 8.6, crystal tracking ID 315086f2, unique puck ID loy8-5

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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: RAYONIX MX-300 / Detector: CCD / Date: Jun 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.8→46.98 Å / Num. obs: 61091 / % possible obs: 99.8 % / Redundancy: 6.209 % / Biso Wilson estimate: 58.184 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.104 / Χ2: 0.923 / Net I/σ(I): 12.65 / Num. measured all: 379292 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.876.3010.6483.2628215447844780.9010.707100
2.87-2.956.30.4854.1727525436943690.9330.529100
2.95-3.046.2940.3795.1226749425142500.9620.414100
3.04-3.136.2880.2956.3625691408640860.9770.322100
3.13-3.236.2950.2257.7725131399339920.9840.245100
3.23-3.356.270.1759.5624439389838980.9890.191100
3.35-3.476.2710.14210.9323335372137210.9920.155100
3.47-3.616.2610.12312.3822565360436040.9930.134100
3.61-3.786.2520.10913.4721608345834560.9950.11999.9
3.78-3.966.2230.09615.0120573330833060.9950.10599.9
3.96-4.176.1970.07917.4719595316331620.9960.087100
4.17-4.436.1810.07418.9118414298029790.9960.081100
4.43-4.736.1550.06720.317307281328120.9960.074100
4.73-5.116.1350.06820.4816233264926460.9960.07499.9
5.11-5.66.1360.06919.5514842242324190.9970.07599.8
5.6-6.266.1170.06819.2113537221722130.9970.07599.8
6.26-7.236.0590.06320.2111937197719700.9970.06999.6
7.23-8.855.9990.05322.989970167216620.9970.05899.4
8.85-12.525.840.05125.447761134313290.9980.05699
12.52-46.985.230.05124.238657807390.9950.05894.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dn8

5dn8


Resolution: 2.8→46.98 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 3118 5.11 %
Rwork0.203 57908 -
obs0.2047 61026 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.59 Å2 / Biso mean: 59.6084 Å2 / Biso min: 20.31 Å2
Refinement stepCycle: final / Resolution: 2.8→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11607 0 233 108 11948
Biso mean--49.97 46.48 -
Num. residues----1560
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6732X-RAY DIFFRACTION10.691TORSIONAL
12B6732X-RAY DIFFRACTION10.691TORSIONAL
13C6732X-RAY DIFFRACTION10.691TORSIONAL
14D6732X-RAY DIFFRACTION10.691TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.840.33941500.278626192769100
2.84-2.890.33641310.260826262757100
2.89-2.940.28411450.246225712716100
2.94-2.990.32211360.244526042740100
2.99-3.050.26341110.253626172728100
3.05-3.110.31941250.277326312756100
3.11-3.180.27321390.24626272766100
3.18-3.260.24661070.22726382745100
3.26-3.340.26041490.219626002749100
3.34-3.430.23041330.207626142747100
3.43-3.530.24541340.200626352769100
3.53-3.640.22011830.20725812764100
3.64-3.770.26571600.201126022762100
3.77-3.920.26761330.206826272760100
3.92-4.10.22371540.181726332787100
4.1-4.320.18741350.166126152750100
4.32-4.590.19911330.157226682801100
4.59-4.940.18991400.155626422782100
4.94-5.440.21381630.177126392802100
5.44-6.220.2171710.219326372808100
6.22-7.830.24661330.224527372870100
7.84-46.980.21781530.19982745289897
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)
13.2168-0.3598-0.97211.12630.36163.28050.06570.0531-0.0476-0.01490.07310.13050.0116-0.2425-0.06790.33250.06550.00150.32190.04680.295-56.95532.8355-85.9232
26.381.32431.79093.54110.40722.3646-0.09790.94050.099-0.1730.3515-0.0506-0.22750.0624-0.21970.3221-0.06040.02710.63630.01820.3059-22.819132.78-7.4415
32.04961.95380.42874.3223-0.28240.7517-0.27980.6675-0.3195-0.13390.3224-0.82080.06430.54190.08060.42680.00970.04790.8781-0.06750.5554-14.625825.7954-10.6273
41.7481-0.50510.00243.39020.91613.26830.0831-0.0269-0.2818-0.15590.1236-0.01560.1774-0.0185-0.19720.31970.0244-0.03810.30930.01150.3275-40.3438.0964-8.9309
55.8531-0.2764-0.08562.90350.40053.24850.18320.95050.3551-0.5242-0.00370.2949-0.0012-0.5229-0.27740.1938-0.1868-0.04880.55660.07810.2336-19.18830.2973-72.1257
64.3849-3.20493.43152.3547-2.49562.67920.45751.0291-0.2633-0.5231-0.3125-0.1324-0.34020.875-0.3460.5593-0.16630.02950.66130.00920.4134-29.787223.0815-79.3259
76.8771-0.17260.71084.19120.60674.1605-0.0142-0.83690.05720.37470.32220.0586-0.10610.1538-0.23180.4307-0.19320.08250.55920.10020.3273-20.313628.1043-66.1734
85.11010.22221.88334.95222.06983.14880.04410.27180.62720.0850.021-0.0591-0.65790.1501-0.02730.3425-0.05950.0230.38360.07440.3653-10.741339.9425-70.2587
96.21227.4959-3.52979.2624-4.60832.88430.1247-0.2086-1.0642-0.2547-0.207-1.05460.08680.74370.15170.48850.0324-0.14690.39850.10170.4373-10.909517.7268-71.4346
103.5261-3.08970.21768.38950.17236.0016-0.0901-0.5328-0.76781.14830.3260.49020.8121-0.1564-0.2370.6165-0.0155-0.06250.71010.20220.4531-32.47116.8224-54.9272
111.4608-0.1116-1.00780.88050.91323.87750.2499-0.8463-0.35980.48580.08190.33640.0394-0.0757-0.26090.3957-0.037-0.0730.45090.21390.4015-31.191112.856-61.7467
122.2562-1.16140.71973.54361.08574.36820.56370.2013-0.7691-0.5756-0.25080.61050.2644-0.3873-0.27610.52660.0355-0.21150.35620.03670.6017-37.60637.24-78.0047
136.87583.35891.12067.0026-0.76583.10150.00560.09280.43730.5027-0.2016-0.2512-0.31080.52250.17690.4774-0.112-0.07230.41910.0460.419-36.002548.4656-25.6893
144.32630.12611.0572.07340.763.07170.14430.30390.3123-0.4233-0.0042-0.1329-0.20510.1253-0.11180.37520.00110.06790.38960.08790.2564-58.993539.4183-33.6843
152.4257-0.6932-0.53361.36840.57984.5787-0.1305-0.5636-0.21340.27460.24070.07070.49330.224-0.10230.33370.052-0.00350.41560.08640.3327-63.046729.5657-15.7773
164.66381.76310.03996.4684-2.13222.46220.2578-0.09350.40910.7652-0.2717-0.1051-0.37890.24390.00160.4943-0.0724-0.00410.3102-0.03170.2992-31.549848.4382-88.4206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 167 through 447 )D167 - 447
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 151 )A15 - 151
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 191 )A152 - 191
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 447 )A192 - 447
5X-RAY DIFFRACTION5chain 'B' and (resid 15 through 37 )B15 - 37
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 59 )B38 - 59
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 97 )B60 - 97
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 166 )B98 - 166
9X-RAY DIFFRACTION9chain 'B' and (resid 167 through 191 )B167 - 191
10X-RAY DIFFRACTION10chain 'B' and (resid 192 through 235 )B192 - 235
11X-RAY DIFFRACTION11chain 'B' and (resid 236 through 287 )B236 - 287
12X-RAY DIFFRACTION12chain 'B' and (resid 288 through 447 )B288 - 447
13X-RAY DIFFRACTION13chain 'C' and (resid 16 through 166 )C16 - 166
14X-RAY DIFFRACTION14chain 'C' and (resid 167 through 287 )C167 - 287
15X-RAY DIFFRACTION15chain 'C' and (resid 288 through 447 )C288 - 447
16X-RAY DIFFRACTION16chain 'D' and (resid 15 through 166 )D15 - 166

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