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- PDB-9zpb: Crystal structure of Phosphoribosylaminoimidazole carboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 9zpb
TitleCrystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (AMP complex)
ComponentsN5-carboxyaminoimidazole ribonucleotide synthase
KeywordsLYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / TRANSFERASE / Phosphoribosylaminoimidazole carboxylase
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / : / Ribonucleotide synthetase preATP-grasp domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / : / Ribonucleotide synthetase preATP-grasp domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesParaburkholderia xenovorans LB400 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (AMP complex)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 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: N5-carboxyaminoimidazole ribonucleotide synthase
B: N5-carboxyaminoimidazole ribonucleotide synthase
C: N5-carboxyaminoimidazole ribonucleotide synthase
D: N5-carboxyaminoimidazole ribonucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,25118
Polymers170,0384
Non-polymers2,21314
Water10,142563
1
A: N5-carboxyaminoimidazole ribonucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0314
Polymers42,5101
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N5-carboxyaminoimidazole ribonucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2736
Polymers42,5101
Non-polymers7645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N5-carboxyaminoimidazole ribonucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9734
Polymers42,5101
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N5-carboxyaminoimidazole ribonucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9734
Polymers42,5101
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.005, 170.156, 170.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
N5-carboxyaminoimidazole ribonucleotide synthase / N5-CAIR synthase / 5-(carboxyamino)imidazole ribonucleotide synthetase


Mass: 42509.523 Da / Num. of mol.: 4 / Fragment: S9-T397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia xenovorans LB400 (bacteria)
Gene: purK, Bxe_A0694 / Plasmid: BuxeA.00036.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q13UJ9, 5-(carboxyamino)imidazole ribonucleotide synthase

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Non-polymers , 7 types, 577 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM AMP, plate 20558 E6 drop 3, Puck: ...Details: BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM AMP, plate 20558 E6 drop 3, Puck: PSL-1916, Cryo: 20% PEG 200 + 80% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 10, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.19→47.22 Å / Num. obs: 101060 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.054 / Rrim(I) all: 0.199 / Χ2: 1.11 / Net I/σ(I): 11.7 / Num. measured all: 1358383
Reflection shellResolution: 2.19→2.25 Å / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 2.188 / Num. measured all: 101556 / Num. unique obs: 7380 / CC1/2: 0.725 / Rpim(I) all: 0.608 / Rrim(I) all: 2.272 / Χ2: 0.99 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5765: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→44.78 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 4920 4.87 %
Rwork0.1738 --
obs0.1752 100938 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11420 0 144 563 12127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811934
X-RAY DIFFRACTIONf_angle_d0.96816292
X-RAY DIFFRACTIONf_dihedral_angle_d134323
X-RAY DIFFRACTIONf_chiral_restr0.0541882
X-RAY DIFFRACTIONf_plane_restr0.0122143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.210.34671620.29483157X-RAY DIFFRACTION100
2.21-2.240.33371450.28063200X-RAY DIFFRACTION100
2.24-2.270.26881580.26563131X-RAY DIFFRACTION100
2.27-2.30.32241720.24583175X-RAY DIFFRACTION100
2.3-2.330.29571510.23473156X-RAY DIFFRACTION100
2.33-2.360.25481790.22963146X-RAY DIFFRACTION100
2.36-2.390.25951590.21873200X-RAY DIFFRACTION100
2.39-2.430.26071600.22473113X-RAY DIFFRACTION100
2.43-2.470.20131520.21783207X-RAY DIFFRACTION100
2.47-2.510.23091850.20953179X-RAY DIFFRACTION100
2.51-2.550.26461890.20533112X-RAY DIFFRACTION100
2.55-2.60.24651830.19993124X-RAY DIFFRACTION100
2.6-2.650.24771890.21643183X-RAY DIFFRACTION100
2.65-2.70.28891560.20673173X-RAY DIFFRACTION100
2.7-2.760.24051900.21363147X-RAY DIFFRACTION100
2.76-2.820.26351450.19183195X-RAY DIFFRACTION100
2.82-2.890.21831640.17783205X-RAY DIFFRACTION100
2.89-2.970.20371400.17253192X-RAY DIFFRACTION100
2.97-3.060.23451630.17663210X-RAY DIFFRACTION100
3.06-3.160.23461660.19283183X-RAY DIFFRACTION100
3.16-3.270.22991760.20133185X-RAY DIFFRACTION100
3.27-3.40.21841570.17563201X-RAY DIFFRACTION100
3.4-3.560.22281250.16563259X-RAY DIFFRACTION100
3.56-3.740.18091600.15363220X-RAY DIFFRACTION100
3.74-3.980.16451690.1423220X-RAY DIFFRACTION100
3.98-4.290.14491580.12743237X-RAY DIFFRACTION100
4.29-4.720.12651610.11593263X-RAY DIFFRACTION100
4.72-5.40.16481850.13253243X-RAY DIFFRACTION100
5.4-6.80.17621540.17383347X-RAY DIFFRACTION100
6.8-44.780.18021670.17063455X-RAY DIFFRACTION100
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)
11.0472-0.3415-0.05920.82570.04140.54530.02470.08950.1370.03870.0324-0.0747-0.01030.2053-00.3377-0.00720.00910.3188-0.01080.3294-22.410647.1667-21.9262
20.45440.0384-0.31830.60080.02220.340.1284-0.103-0.07360.1198-0.05780.1596-0.0775-0.025700.36730.0184-0.03390.3987-0.00190.3935-48.429844.1804-29.4617
31.2117-0.31850.08261.0921-0.36830.5657-0.00690.0754-0.1103-0.0869-0.01530.11520.0369-0.059800.30380.0228-0.00330.34-0.06270.3026-28.514127.9558-21.7686
40.1313-0.0980.13450.1223-0.10720.1349-0.12440.11190.01830.10180.06610.19-0.0981-0.019800.38280.0578-0.01550.4263-0.05880.3848-14.697328.06630.0521
50.61570.06210.27430.20170.01251.0113-0.0593-0.07790.03020.19-0.0139-0.0049-0.0756-0.073-00.38520.0175-0.02740.3827-0.0290.33-6.328125.79138.5026
60.4488-0.35320.16740.3090.00960.6626-0.00840.2627-0.0376-0.0037-0.0234-0.17430.06790.385800.38090.0417-0.05140.5349-0.02140.38119.23889.01188.0444
70.4120.02690.34890.485-0.34330.57450.04080.0149-0.06280.0182-0.0373-0.0080.10810.0686-00.34220.0325-0.0010.3566-0.03480.3065-2.511912.4811-6.3022
80.92160.30660.02410.4016-0.280.26890.06570.10450.0155-0.11460.023-0.1252-0.00990.188100.30780.00640.02830.4543-0.04120.35553.86128.2381-20.2616
90.4505-0.0608-0.22231.44830.39780.9699-0.06630.1317-0.20340.0326-0.0770.02040.135-0.0629-00.3479-0.00490.02460.3489-0.08820.4019-1.3492-17.7713-52.552
100.59840.0215-0.08120.51430.4010.3270.064-0.04140.02710.00920.07550.00190.1080.2255-00.3958-0.03060.02960.406-0.06970.397328.1416-7.585-57.8881
110.5539-0.1006-0.42690.57570.04041.285-0.0328-0.09340.171-0.00880.1248-0.1214-0.09130.29860.01080.32890.036-0.00890.396-0.13280.39718.6796-4.6264-38.2031
120.0245-0.06160.07970.2824-0.17420.25740.3070.2259-0.2051-0.4719-0.0990.04260.4113-0.038300.71360.0726-0.09520.3927-0.09060.5883-5.8185-25.8959-26.942
130.1195-0.2607-0.17291.1611-0.19691.55240.0944-0.217-0.13710.07080.01350.4420.3579-0.51980.00270.4622-0.1412-0.02260.50680.01190.5467-23.4509-20.2151-10.6172
140.57930.11710.62110.51410.0611.12990.0091-0.0543-0.00890.0801-0.03240.05860.0807-0.225200.38290.0139-0.00540.4251-0.09450.4042-16.7635-8.2174-22.6879
150.36520.01650.24410.0984-0.010.1644-0.0118-0.10630.17440.09160.02050.1889-0.0902-0.339900.3516-0.0082-0.0280.4634-0.09150.4455-22.2111-4.4735-34.057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 143 )
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 195 )
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 397 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 35 )
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 123 )
6X-RAY DIFFRACTION6chain 'B' and (resid 124 through 183 )
7X-RAY DIFFRACTION7chain 'B' and (resid 184 through 330 )
8X-RAY DIFFRACTION8chain 'B' and (resid 331 through 397 )
9X-RAY DIFFRACTION9chain 'C' and (resid 8 through 122 )
10X-RAY DIFFRACTION10chain 'C' and (resid 123 through 195 )
11X-RAY DIFFRACTION11chain 'C' and (resid 196 through 396 )
12X-RAY DIFFRACTION12chain 'D' and (resid 8 through 59 )
13X-RAY DIFFRACTION13chain 'D' and (resid 60 through 225 )
14X-RAY DIFFRACTION14chain 'D' and (resid 226 through 357 )
15X-RAY DIFFRACTION15chain 'D' and (resid 358 through 397 )

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