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- PDB-5vk4: Crystal structure of a phosphoribosylformylglycinamidine cyclo-li... -

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Entry
Database: PDB / ID: 5vk4
TitleCrystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from Neisseria gonorrhoeae bound to AMPPNP and magnesium
ComponentsPhosphoribosylformylglycinamidine cyclo-ligase
KeywordsLIGASE / structural genomics / ATP-dependent / non-hydrolyzable substrate analog / purM / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from Neisseria gonorrhoeae bound to AMPPNP and magnesium
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine cyclo-ligase
B: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0296
Polymers75,9682
Non-polymers1,0614
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-47 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.250, 79.610, 150.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 15 through 28 or (resid 29...
21(chain B and (resid 15 through 38 or resid 45...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPALAALA(chain A and (resid 15 through 28 or (resid 29...AA15 - 2823 - 36
12LYSLYSARGARG(chain A and (resid 15 through 28 or (resid 29...AA29 - 3037 - 38
13ASPASPANPANP(chain A and (resid 15 through 28 or (resid 29...AA - C15 - 40123
14ASPASPANPANP(chain A and (resid 15 through 28 or (resid 29...AA - C15 - 40123
15ASPASPANPANP(chain A and (resid 15 through 28 or (resid 29...AA - C15 - 40123
16ASPASPANPANP(chain A and (resid 15 through 28 or (resid 29...AA - C15 - 40123
21ASPASPGLYGLY(chain B and (resid 15 through 38 or resid 45...BB15 - 3823 - 46
22ALAALAGLYGLY(chain B and (resid 15 through 38 or resid 45...BB45 - 5053 - 58
23LYSLYSLYSLYS(chain B and (resid 15 through 38 or resid 45...BB51 - 5259 - 60
24ASPASPANPANP(chain B and (resid 15 through 38 or resid 45...BB - E15 - 40123
25ASPASPANPANP(chain B and (resid 15 through 38 or resid 45...BB - E15 - 40123
26ASPASPANPANP(chain B and (resid 15 through 38 or resid 45...BB - E15 - 40123
27ASPASPANPANP(chain B and (resid 15 through 38 or resid 45...BB - E15 - 40123

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Components

#1: Protein Phosphoribosylformylglycinamidine cyclo-ligase / AIR synthase / AIRS / Phosphoribosyl-aminoimidazole synthetase


Mass: 37984.227 Da / Num. of mol.: 2 / Fragment: UNP residues 1-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria)
Gene: purM, WHOG_01214C, WHOG_02062, WHON_01216C, WHON_01605, WHOO_01146C, WHOO_02090
Production host: Escherichia coli (E. coli)
References: UniProt: A0A1D3FYK6, UniProt: Q5F973*PLUS, phosphoribosylformylglycinamidine cyclo-ligase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NegoA.00263.a.B1.PW37900 at 18.3 mg/mL with 3 mM MgCl2 and 3 mM AMPPNP against MCSG1 screen condition B4 which contains 0.2 M MgCl2, 0.1 M BisTris pH 6.5, and 25% PEG 3350, supplemented with ...Details: NegoA.00263.a.B1.PW37900 at 18.3 mg/mL with 3 mM MgCl2 and 3 mM AMPPNP against MCSG1 screen condition B4 which contains 0.2 M MgCl2, 0.1 M BisTris pH 6.5, and 25% PEG 3350, supplemented with 15% EG as cryo protectant,crystal tracking ID 273610b4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→44.831 Å / Num. obs: 19414 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.003 % / Biso Wilson estimate: 47.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.092 / Χ2: 1.028 / Net I/σ(I): 15.35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.725.110.6292.6714210.8060.70499.9
2.72-2.795.1480.4843.5113500.8480.54499.8
2.79-2.875.120.4094.0713720.8630.45999.9
2.87-2.965.1170.3424.9613040.9020.38499.5
2.96-3.065.1140.2616.4112600.9340.29499.6
3.06-3.175.0770.2027.8912260.9670.22799.7
3.17-3.295.1120.14510.8411730.9840.16399.4
3.29-3.425.040.11713.2111530.9860.13299.1
3.42-3.575.0320.09915.4110910.9890.11299.2
3.57-3.755.0350.07918.4110440.9940.08999.1
3.75-3.954.990.06620.7810150.9950.07499.3
3.95-4.194.8830.05524.429540.9960.06298.7
4.19-4.484.9570.04828.28750.9960.05598.3
4.48-4.844.9180.04628.438340.9970.05298.2
4.84-5.34.9060.042297800.9980.04799
5.3-5.934.9150.04727.676970.9960.05297.9
5.93-6.844.7640.04327.846390.9980.04999.5
6.84-8.384.7430.03432.75410.9990.03899.6
8.38-11.854.5370.02937.724360.9990.03299.5
11.85-44.83140.02636.082490.9980.02993.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXdev_2744refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CLI

1cli


Resolution: 2.65→44.831 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 24.96
RfactorNum. reflection% reflection
Rfree0.2443 978 5.04 %
Rwork0.1846 --
obs0.1876 19411 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.55 Å2 / Biso mean: 53.0209 Å2 / Biso min: 17.36 Å2
Refinement stepCycle: final / Resolution: 2.65→44.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 64 51 4842
Biso mean--73.63 41.67 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054875
X-RAY DIFFRACTIONf_angle_d0.7586654
X-RAY DIFFRACTIONf_chiral_restr0.05778
X-RAY DIFFRACTIONf_plane_restr0.006863
X-RAY DIFFRACTIONf_dihedral_angle_d14.6582833
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2776X-RAY DIFFRACTION8.029TORSIONAL
12B2776X-RAY DIFFRACTION8.029TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.78970.32551360.261925812717100
2.7897-2.96450.32891480.246426002748100
2.9645-3.19330.30091230.233726362759100
3.1933-3.51450.29091340.21292576271099
3.5145-4.02280.2281520.17232621277399
4.0228-5.06720.19241330.14242645277898
5.0672-44.8370.21721520.16352774292699
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)
19.9034-1.3013-1.89257.54011.67186.9736-0.3230.7118-0.8298-0.29460.36950.42380.43150.1066-0.03590.2879-0.029-0.06080.2589-0.05170.4703-3.9763-18.3897-9.572
24.9159-0.02222.30865.28730.40883.92150.05210.01240.2529-0.1252-0.10781.1245-0.0667-0.41630.05370.2823-0.0017-0.01150.23250.05260.4465-14.79940.8648-6.0888
33.4264-2.32570.60514.8553-0.25082.1824-0.12270.0765-0.20140.050.09660.00280.1130.06270.01240.2403-0.0160.02080.1660.00260.29030.9373-7.8172-0.7523
41.1241-0.15070.21062.42030.05711.3167-0.2511-0.38490.16390.66320.3602-0.2715-0.0252-0.0853-0.10760.52360.17020.04240.3091-0.00230.3381-6.4216.460215.791
55.9596-0.56531.5598.0933-3.72119.0324-0.1937-0.7863-0.53851.29440.1756-0.592-0.22860.32980.0430.57940.1761-0.05890.54040.02330.474612.7537-13.089919.1556
62.5769-1.02140.00473.56270.67162.5453-0.3425-0.51740.02090.78990.3595-0.0416-0.12750.1083-0.02510.53020.14580.05910.3490.06070.2769-3.34444.022419.5905
73.51530.23211.53842.42551.21061.35-0.1157-0.59171.27230.5903-0.0923-0.2982-0.448-0.13390.26170.5864-0.0102-0.10380.3160.02660.58043.671716.1736-4.3119
88.22680.8633-0.65744.88262.22885.6330.04770.20220.71440.193-0.2990.5989-0.3061-0.63780.32390.3630.01030.07380.26030.07360.2899-11.14396.8016-9.6393
92.6486-0.5523-0.10982.1927-0.14212.7987-0.22090.93940.1282-0.2131-0.128-0.2681-0.27260.74910.24270.2716-0.08880.00950.42430.05030.3178.44863.4967-14.4765
105.81-0.28120.62632.7849-0.85363.52940.17550.3439-0.1013-0.0331-0.261-0.2276-0.29990.43510.08760.3219-0.0313-0.03460.16840.02350.32586.33965.6248-9.6285
112.3960.20920.14111.2097-0.15932.8149-0.02041.255-0.2846-0.40690.08090.42910.39480.2738-0.04670.5991-0.02-0.14530.775-0.10140.4449-3.5542-1.8358-31.2299
122.68991.1827-1.61811.66150.61522.5263-0.05420.9984-0.3327-0.886-0.2536-0.79040.08470.6440.29720.55090.13730.17471.0540.13930.684223.7536-0.3826-28.4621
131.9387-0.2673-0.59661.88520.28292.9501-0.0991.3068-0.4213-0.5065-0.0890.14490.32210.26960.18480.55510.01230.01260.8713-0.10050.36322.913-1.2101-31.6293
144.7201-0.22310.92641.5236-1.22142.70370.24721.5563-0.265-0.4716-0.24030.16740.10870.4792-0.0340.5587-0.0325-0.0261.1204-0.08410.34450.7908-1.4678-35.6371
153.45511.40430.04713.6276-1.092.51460.12451.6682-0.7705-0.39490.0025-0.15241.00280.3862-0.03650.9479-0.0436-0.07461.0031-0.29480.5436-3.3124-6.8075-38.2609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 31 )A15 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 64 )A32 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 166 )A65 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 191 )A167 - 191
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 215 )A192 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 344 )A216 - 344
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 41 )B15 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 64 )B42 - 64
9X-RAY DIFFRACTION9chain 'B' and (resid 65 through 113 )B65 - 113
10X-RAY DIFFRACTION10chain 'B' and (resid 114 through 166 )B114 - 166
11X-RAY DIFFRACTION11chain 'B' and (resid 167 through 191 )B167 - 191
12X-RAY DIFFRACTION12chain 'B' and (resid 192 through 215 )B192 - 215
13X-RAY DIFFRACTION13chain 'B' and (resid 216 through 285 )B216 - 285
14X-RAY DIFFRACTION14chain 'B' and (resid 286 through 320 )B286 - 320
15X-RAY DIFFRACTION15chain 'B' and (resid 321 through 344 )B321 - 344

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