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- PDB-9rb1: Streptococcus pyogenes GapN in complex with 2-cyanoacetamide -

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Basic information

Entry
Database: PDB / ID: 9rb1
TitleStreptococcus pyogenes GapN in complex with 2-cyanoacetamide
ComponentsNADP-dependent glyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GapN / Fragment screening / Soaking
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity
Similarity search - Function
: / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
2-cyanoacetamide / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsWirsing, R. / Schindelin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Streptococcus pyogenes GapN in complex with 2-cyanoacetamide
Authors: Wirsing, R. / Schindelin, H.
History
DepositionMay 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,04845
Polymers423,6738
Non-polymers3,37537
Water80,6174475
1
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,38621
Polymers211,8374
Non-polymers1,54917
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19030 Å2
ΔGint-214 kcal/mol
Surface area61370 Å2
MethodPISA
2
E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,66224
Polymers211,8374
Non-polymers1,82620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19260 Å2
ΔGint-192 kcal/mol
Surface area60810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.517, 99.583, 104.162
Angle α, β, γ (deg.)77.660, 75.940, 67.670
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 52959.152 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: E0F67_08075 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4U9C786
#2: Chemical
ChemComp-XHD / 2-cyanoacetamide


Mass: 84.077 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H4N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4475 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: BisTris buffer pH 6.7 Li2SO4 polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.61→47.92 Å / Num. obs: 437149 / % possible obs: 70.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.048 / Net I/σ(I): 10.2
Reflection shellResolution: 1.61→1.668 Å / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 1875 / CC1/2: 0.485 / Rpim(I) all: 0.686 / Rrim(I) all: 1.247 / % possible all: 4.11

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→47.92 Å / SU ML: 0.1416 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1932 16197 5.03 %
Rwork0.1571 305583 -
obs0.1589 321780 70.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.69 Å2
Refinement stepCycle: LAST / Resolution: 1.61→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28368 0 206 4475 33049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004529382
X-RAY DIFFRACTIONf_angle_d0.718939928
X-RAY DIFFRACTIONf_chiral_restr0.04734701
X-RAY DIFFRACTIONf_plane_restr0.00645163
X-RAY DIFFRACTIONf_dihedral_angle_d12.624510796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.4946130.3134292X-RAY DIFFRACTION2.03
1.63-1.650.3172410.2615543X-RAY DIFFRACTION3.82
1.65-1.670.2791420.2713854X-RAY DIFFRACTION5.9
1.67-1.690.2868740.2751361X-RAY DIFFRACTION9.35
1.69-1.710.32711000.26951978X-RAY DIFFRACTION13.74
1.71-1.730.36841490.27422578X-RAY DIFFRACTION17.84
1.73-1.760.30071880.26083488X-RAY DIFFRACTION24.15
1.76-1.780.28712500.24954671X-RAY DIFFRACTION32.29
1.78-1.810.31323380.24236258X-RAY DIFFRACTION43.31
1.81-1.840.28024570.24148633X-RAY DIFFRACTION59.69
1.84-1.870.26615760.227311020X-RAY DIFFRACTION75.88
1.87-1.910.26076870.220412307X-RAY DIFFRACTION85.32
1.91-1.940.25627080.216613094X-RAY DIFFRACTION90.33
1.94-1.980.24777580.201813554X-RAY DIFFRACTION94.13
1.98-2.030.25567680.194413768X-RAY DIFFRACTION95.25
2.03-2.070.23477630.18613964X-RAY DIFFRACTION96.37
2.07-2.120.2117420.172313482X-RAY DIFFRACTION93.02
2.12-2.180.21247240.157813924X-RAY DIFFRACTION96.46
2.18-2.250.19797310.153514105X-RAY DIFFRACTION96.97
2.25-2.320.19186800.149414144X-RAY DIFFRACTION97.13
2.32-2.40.19637680.15114071X-RAY DIFFRACTION97.3
2.4-2.50.19676900.153914174X-RAY DIFFRACTION97.57
2.5-2.610.19327420.153314168X-RAY DIFFRACTION97.58
2.61-2.750.20557160.153314170X-RAY DIFFRACTION97.71
2.75-2.920.18857360.164914114X-RAY DIFFRACTION97.57
2.92-3.150.18377600.161114123X-RAY DIFFRACTION97.31
3.15-3.460.19517260.149114226X-RAY DIFFRACTION97.94
3.46-3.970.16337520.129814193X-RAY DIFFRACTION98.12
3.97-4.990.13517240.110314218X-RAY DIFFRACTION97.89
4.99-47.920.15897940.147714108X-RAY DIFFRACTION97.78
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)
10.104136526860.03721086765060.02638695314720.188341150424-0.004357927136260.31881087466-0.004743444432550.04470973721980.0236426000706-0.0492953244925-0.008934003980770.0166748453248-0.05032893722610.07284008243-4.36110474584E-70.126430431352-0.00653700033898-0.003561411455990.153046714520.01098760193320.0993959899556-15.2151626949-10.1290484989-50.6524981245
20.326883508494-0.003306782377820.1009698314740.05836646093550.02205784192590.120183444692-0.004455157858750.07364818796220.0159068428887-0.007678190745380.00196683079789-0.000348473138153-0.007404209344320.0390818986693-6.69955275342E-70.123712841548-0.009240702380380.00179121491980.1550544521260.01285949396760.11568240214710.0148520566-29.9252787186-34.1288923311
30.169205927401-0.0505663567463-0.0204168105380.1011821958710.005884288413620.182472956529-0.01966560149190.003400091190270.01691597623750.01444008486080.002012705632220.00294930253054-0.0129585456464-0.0179529519742-1.11606915842E-60.113002688879-0.01079238549220.00411058719240.0962733449197-0.006317085444490.107555924845-31.8096307219-21.3370002971-8.13060820802
40.222822992390.1116605882670.009863671296430.204481929544-0.03144044851240.129485015618-0.0005679973079520.0156298953618-0.0238606975042-0.006399747122090.00820158795616-0.002713135167270.0133758596668-0.0167979634349-2.64732485431E-70.109299504448-0.01017180900010.006077968793040.128965306104-0.02037220397810.112811973404-30.9218528621-51.5839364991-27.7231557584
50.152770120458-0.0410814627338-0.1303994176830.1648162100760.06870552569650.455649026884-0.0724702703536-0.0535636878232-0.03949174181380.1069255541790.04083160961010.05381823226620.08686905248850.0563012046979-0.0486792638040.18121611950.02831424030480.03099312874290.1375422788720.03028128057280.144784558858-3.53108120196-87.8151239594-56.845954052
60.770006219243-0.2598702100250.04010245842670.2033216474270.002323357067990.1241506909520.00763760540758-0.0635043299034-0.220154937388-0.01150456483810.0173986810590.126319028197-0.00341020760017-0.00110801412280.08649032907570.118187426744-0.005760810556270.001495834087560.1068481417340.03728383665320.206331977031-28.7408464932-80.2887431867-81.5258759353
70.1673670180960.02047263044880.06121666264650.211512286626-0.03817074688580.144915434876-0.0166439522783-0.006252194712710.0148567521120.0162564182015-0.00496089333976-0.0151731537064-0.01214568181240.00229506637915-6.03470993688E-70.120687474933-0.002782213423180.009259800301970.111545275414-0.0046901860350.11395131491213.1368680121-52.5789202811-82.7693063361
80.217572772066-0.0409059954511-0.09414116080380.07346831162610.03869594289340.204141551162-0.0003180934847050.0134341945752-0.0262037360745-0.00579693019155-0.007945447257350.02173447427550.003090247942390.00912684165173-8.51044262594E-70.1213538384770.00407525897166-0.0006588932276250.10199521242-0.005283032671980.13000769554512.2858446053-81.7615826539-104.020293048
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 2 through 504)AA2 - 504
22(chain 'B' and resid 2 through 504)BB2 - 504
33(chain 'C' and resid 1 through 504)CC1 - 504
44(chain 'D' and resid 1 through 505)DD1 - 505
55(chain 'E' and resid 2 through 504)EE2 - 504
66(chain 'F' and resid 2 through 504)FF2 - 504
77(chain 'G' and resid 1 through 506)GG1 - 506
88(chain 'H' and resid 1 through 506)HH1 - 506

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