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- PDB-9uly: crystal structure of AbGHMP in complex with L-Ara and AMPPNP -

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Basic information

Entry
Database: PDB / ID: 9uly
Titlecrystal structure of AbGHMP in complex with L-Ara and AMPPNP
ComponentsAbGHMP
KeywordsTRANSFERASE / arabinokinase
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / beta-L-arabinopyranose
Function and homology information
Biological speciesAcidobacteriota (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHe, C. / Li, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: crystal structure of apo AbGHMP
Authors: He, C. / Li, F.
History
DepositionApr 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AbGHMP
B: AbGHMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1118
Polymers107,7492
Non-polymers1,3616
Water00
1
A: AbGHMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5554
Polymers53,8751
Non-polymers6813
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-4 kcal/mol
Surface area19710 Å2
MethodPISA
2
B: AbGHMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5554
Polymers53,8751
Non-polymers6813
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-4 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.356, 112.146, 89.922
Angle α, β, γ (deg.)90.00, 93.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AbGHMP


Mass: 53874.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidobacteriota (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Sugar ChemComp-ARB / beta-L-arabinopyranose / beta-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LArapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinopyranoseCOMMON NAMEGMML 1.0
b-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl buffer at pH 8.5, with 25% (w/v) polyethylene glycol (PEG) 1,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→49.54 Å / Num. obs: 33783 / % possible obs: 96.9 % / Redundancy: 4.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.054 / Rrim(I) all: 0.115 / Χ2: 0.96 / Net I/σ(I): 9 / Num. measured all: 138618
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 98.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.837 / Num. measured all: 17202 / Num. unique obs: 4184 / CC1/2: 0.7 / Rpim(I) all: 0.452 / Rrim(I) all: 0.958 / Χ2: 0.94 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→41.68 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1736 5.14 %
Rwork0.2076 --
obs0.2103 33743 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7287 0 84 0 7371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027527
X-RAY DIFFRACTIONf_angle_d0.46510232
X-RAY DIFFRACTIONf_dihedral_angle_d16.232788
X-RAY DIFFRACTIONf_chiral_restr0.0391135
X-RAY DIFFRACTIONf_plane_restr0.0051338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.38961670.33592662X-RAY DIFFRACTION98
2.68-2.760.3621360.2962690X-RAY DIFFRACTION98
2.76-2.860.33081430.27622716X-RAY DIFFRACTION98
2.86-2.980.28591270.25722682X-RAY DIFFRACTION97
2.98-3.110.28351140.27242702X-RAY DIFFRACTION97
3.11-3.280.2951340.24892684X-RAY DIFFRACTION97
3.28-3.480.33361570.24082643X-RAY DIFFRACTION96
3.48-3.750.28281690.21952659X-RAY DIFFRACTION97
3.75-4.130.22191510.18982659X-RAY DIFFRACTION96
4.13-4.720.23171880.16432616X-RAY DIFFRACTION96
4.72-5.950.21331200.17932640X-RAY DIFFRACTION95
5.95-41.680.21461300.16882654X-RAY DIFFRACTION93
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)
13.1608-1.4375-1.10382.20420.9462.55790.41410.6581-0.4864-0.4058-0.5690.20720.1495-0.08030.0770.46940.1342-0.11370.592-0.13310.36421.4918-2.918632.1377
23.0694-0.7974-1.17641.66650.26352.9979-0.22610.2903-1.0812-0.0891-0.02980.34460.458-0.28310.1570.4158-0.06480.00620.3346-0.07480.6847.6744-2.604156.4084
32.6305-1.2761-0.99881.0980.25241.59890.0179-0.1281-0.34720.0631-0.0024-0.00690.10970.3517-0.08720.3366-0.0604-0.03670.3444-0.02610.382721.41764.733954.4497
40.50090.5677-0.08621.0544-1.43011.5595-0.0036-1.57582.25070.61290.4086-0.1156-0.7219-0.50230.16990.71580.15280.120.9211-0.79841.7598-2.560544.692683.0113
51.7263-1.80431.71445.4102-1.5171.6176-0.0513-1.2139-0.20030.26930.39321.0228-0.39730.46130.25951.162-0.23310.22642.741-0.98031.22532.348639.0078101.5124
62.78650.3321-1.88482.6819-0.39612.05020.2023-1.63841.85440.5221-0.15060.1242-0.4317-0.35670.17990.6587-0.12240.07891.1637-0.6531.0738.049538.197284.6466
77.9308-2.98272.17271.6603-1.34390.89970.1603-1.2137-0.3673-0.21030.13590.43230.33460.3357-0.31380.4265-0.0020.03620.66580.02060.40887.700917.392282.3257
83.9354-0.2541-0.49352.6485-0.26392.933-0.0712-1.0831-0.10740.26620.16420.00160.06460.3377-0.11330.27590.01690.02420.5529-0.00240.269519.951313.811381.7915
95.4076-0.6539-0.17011.2396-0.14812.7042-0.0503-0.34380.50320.03330.13370.2031-0.1647-0.3148-0.01120.3805-0.0233-0.03280.2151-0.04390.5126-4.286724.915270.4019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 246 )
2X-RAY DIFFRACTION2chain 'A' and (resid 247 through 315 )
3X-RAY DIFFRACTION3chain 'A' and (resid 316 through 489 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 80 )
5X-RAY DIFFRACTION5chain 'B' and (resid 81 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 246 )
7X-RAY DIFFRACTION7chain 'B' and (resid 247 through 282 )
8X-RAY DIFFRACTION8chain 'B' and (resid 283 through 371 )
9X-RAY DIFFRACTION9chain 'B' and (resid 372 through 489 )

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