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- PDB-6c6b: Co-crystal structure of adenylyl-sulfate kinase from Cryptococcus... -

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Basic information

Entry
Database: PDB / ID: 6c6b
TitleCo-crystal structure of adenylyl-sulfate kinase from Cryptococcus neoformans bound to ADP
ComponentsAdenylyl-sulfate kinase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Adenylylsulphate kinase / Adenylyl-sulfate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylyl-sulfate kinase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Adenylyl-sulfate kinase bound to ADP
Authors: Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Adenylyl-sulfate kinase
B: Adenylyl-sulfate kinase
C: Adenylyl-sulfate kinase
D: Adenylyl-sulfate kinase
E: Adenylyl-sulfate kinase
F: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,53415
Polymers139,7856
Non-polymers2,7499
Water7,116395
1
A: Adenylyl-sulfate kinase
B: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6357
Polymers46,5952
Non-polymers1,0415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-28 kcal/mol
Surface area17110 Å2
MethodPISA
2
C: Adenylyl-sulfate kinase
F: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4494
Polymers46,5952
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-34 kcal/mol
Surface area16770 Å2
MethodPISA
3
D: Adenylyl-sulfate kinase
E: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4494
Polymers46,5952
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-29 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.330, 86.330, 160.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 8 and (name N or name...
21(chain B and ((resid 8 and (name N or name...
31(chain C and ((resid 8 and (name N or name...
41(chain D and ((resid 8 and (name N or name...
51(chain E and (resid 8:23 or (resid 24 and (name...
61(chain F and ((resid 8 and (name N or name...

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
11HISHISHISHIS(chain A and ((resid 8 and (name N or name...AA816
12ASNASNALAALA(chain A and ((resid 8 and (name N or name...AA4 - 20312 - 211
13ASNASNALAALA(chain A and ((resid 8 and (name N or name...AA4 - 20312 - 211
14ASNASNALAALA(chain A and ((resid 8 and (name N or name...AA4 - 20312 - 211
15ASNASNALAALA(chain A and ((resid 8 and (name N or name...AA4 - 20312 - 211
21HISHISHISHIS(chain B and ((resid 8 and (name N or name...BB816
22ALAALAALAALA(chain B and ((resid 8 and (name N or name...BB2 - 20310 - 211
23ALAALAALAALA(chain B and ((resid 8 and (name N or name...BB2 - 20310 - 211
24ALAALAALAALA(chain B and ((resid 8 and (name N or name...BB2 - 20310 - 211
25ALAALAALAALA(chain B and ((resid 8 and (name N or name...BB2 - 20310 - 211
31HISHISHISHIS(chain C and ((resid 8 and (name N or name...CC816
32PHEPHEALAALA(chain C and ((resid 8 and (name N or name...CC7 - 20315 - 211
33PHEPHEALAALA(chain C and ((resid 8 and (name N or name...CC7 - 20315 - 211
34PHEPHEALAALA(chain C and ((resid 8 and (name N or name...CC7 - 20315 - 211
35PHEPHEALAALA(chain C and ((resid 8 and (name N or name...CC7 - 20315 - 211
41HISHISHISHIS(chain D and ((resid 8 and (name N or name...DD816
42HISHISALAALA(chain D and ((resid 8 and (name N or name...DD8 - 20316 - 211
43HISHISALAALA(chain D and ((resid 8 and (name N or name...DD8 - 20316 - 211
44HISHISALAALA(chain D and ((resid 8 and (name N or name...DD8 - 20316 - 211
45HISHISALAALA(chain D and ((resid 8 and (name N or name...DD8 - 20316 - 211
51HISHISGLNGLN(chain E and (resid 8:23 or (resid 24 and (name...EE8 - 2316 - 31
52LYSLYSLYSLYS(chain E and (resid 8:23 or (resid 24 and (name...EE2432
53HISHISPROPRO(chain E and (resid 8:23 or (resid 24 and (name...EE8 - 20216 - 210
54HISHISPROPRO(chain E and (resid 8:23 or (resid 24 and (name...EE8 - 20216 - 210
55HISHISPROPRO(chain E and (resid 8:23 or (resid 24 and (name...EE8 - 20216 - 210
56HISHISPROPRO(chain E and (resid 8:23 or (resid 24 and (name...EE8 - 20216 - 210
61HISHISHISHIS(chain F and ((resid 8 and (name N or name...FF816
62ILEILEALAALA(chain F and ((resid 8 and (name N or name...FF5 - 20313 - 211
63ILEILEALAALA(chain F and ((resid 8 and (name N or name...FF5 - 20313 - 211
64ILEILEALAALA(chain F and ((resid 8 and (name N or name...FF5 - 20313 - 211
65ILEILEALAALA(chain F and ((resid 8 and (name N or name...FF5 - 20313 - 211

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Components

#1: Protein
Adenylyl-sulfate kinase


Mass: 23297.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02202 / Plasmid: CrneC.00830.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J9VMZ3, adenylyl-sulfate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 18.6 mg/mL CrneC.00830.a.B1, PS38292 with JCSG+ A8 (0.2 M ammonium formate, 20% w/v PEG3350, 5 mM magnesium chloride, 5 mM ADP), cryoprotectant: 20% ethylene glycol, 5 mM magnesium chloride, ...Details: 18.6 mg/mL CrneC.00830.a.B1, PS38292 with JCSG+ A8 (0.2 M ammonium formate, 20% w/v PEG3350, 5 mM magnesium chloride, 5 mM ADP), cryoprotectant: 20% ethylene glycol, 5 mM magnesium chloride, 5 mM ADP, tray 295929, puck gmh8-1

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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 225 mm CCD / Detector: CCD / Date: Nov 16, 2017 / Details: Beryllium Lenses
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→30.662 Å / Num. obs: 90486 / % possible obs: 99.9 % / Redundancy: 3.84 % / Biso Wilson estimate: 33.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.067 / Χ2: 1.007 / Net I/σ(I): 14.5 / Num. measured all: 347491 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.053.8550.5752.2567710.7070.66799.9
2.05-2.113.8630.4392.9765110.7930.5199.9
2.11-2.173.8680.3573.7162970.8410.41599.9
2.17-2.243.8730.2954.5261910.8940.343100
2.24-2.313.860.2176.159920.9430.25299.9
2.31-2.393.8690.1787.4457740.9610.20699.9
2.39-2.483.8720.1478.8755550.9720.17199.9
2.48-2.583.8540.11711.0253500.9820.13699.9
2.58-2.73.850.09613.5151780.9860.11299.9
2.7-2.833.8530.07616.7148930.990.08899.9
2.83-2.983.8250.06419.4447070.9930.07499.9
2.98-3.163.8160.05622.5543820.9940.06599.8
3.16-3.383.8030.04825.3241740.9950.05599.9
3.38-3.653.7930.04228.6138640.9960.04999.9
3.65-43.7870.03830.7735580.9970.04599.9
4-4.473.7910.03632.3432060.9970.04199.9
4.47-5.163.8130.03632.9128440.9970.04199.9
5.16-6.323.8090.03532.4223830.9970.0499.8
6.32-8.943.7990.03433.4818570.9980.0499.8
8.94-30.6623.6630.03433.739990.9970.03998

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2499refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B8V

6b8v


Resolution: 2→30.662 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 27.89
RfactorNum. reflection% reflection
Rfree0.2672 1946 2.15 %
Rwork0.2243 --
obs0.2252 90466 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.2 Å2 / Biso mean: 47.9353 Å2 / Biso min: 10.41 Å2
Refinement stepCycle: final / Resolution: 2→30.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8838 0 174 403 9415
Biso mean--51.07 41.11 -
Num. residues----1168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089200
X-RAY DIFFRACTIONf_angle_d0.97612553
X-RAY DIFFRACTIONf_chiral_restr0.0581467
X-RAY DIFFRACTIONf_plane_restr0.0061608
X-RAY DIFFRACTIONf_dihedral_angle_d13.5555463
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5033X-RAY DIFFRACTION4.82TORSIONAL
12B5033X-RAY DIFFRACTION4.82TORSIONAL
13C5033X-RAY DIFFRACTION4.82TORSIONAL
14D5033X-RAY DIFFRACTION4.82TORSIONAL
15E5033X-RAY DIFFRACTION4.82TORSIONAL
16F5033X-RAY DIFFRACTION4.82TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0001-2.05010.36831180.278464026520
2.0501-2.10550.28451180.256463586476
2.1055-2.16740.30081120.244662866398
2.1674-2.23740.27731470.24463246471
2.2374-2.31730.24891220.228463266448
2.3173-2.41010.27851740.227763336507
2.4101-2.51970.28221640.221762696433
2.5197-2.65250.25191340.223563206454
2.6525-2.81860.25731680.227363076475
2.8186-3.0360.29971390.233163206459
3.036-3.34120.29751430.233763146457
3.3412-3.82390.24251660.221662986464
3.8239-4.81470.26161040.200563796483
4.8147-30.66580.24631370.222262846421
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)
19.0362-1.72116.71198.30260.6487.76570.6119-1.77040.14860.1716-0.53480.0160.5694-0.6663-0.04960.3593-0.03080.02870.53750.1830.8966-17.356911.3234-22.3168
23.8621-0.1871.63633.6016-0.18491.93480.1778-0.012-0.2298-0.1833-0.2061-0.43890.41180.050.01910.48360.02050.07050.27230.06970.46545.22498.5196-17.5912
33.74761.6181-0.87922.4576-0.1092.16-0.14160.0055-0.3126-0.01150.25790.0270.12470.182-0.16660.31410.0322-0.01260.2352-0.04320.30834.551520.5637-24.1483
45.6117-0.23041.37684.8781-0.36051.2085-0.1357-0.613-0.40860.3940.1089-0.4205-0.1613-0.08620.03520.61030.13450.00010.38680.04850.36210.05317.5742-11.5652
59.1753-0.4248-4.18681.9185-0.37113.4774-1.1698-0.2905-0.20270.42610.62330.08870.62870.23170.52590.69120.13160.07570.44420.1220.5156-0.35642.9081-10.5269
61.50521.0174-0.89081.6805-0.74132.62460.2342-0.00820.23490.00670.04250.1283-0.4371-0.0802-0.27630.32530.09440.02850.2423-0.03970.217727.7969-11.6577-20.582
71.5629-3.26670.03579.2668-0.3742.395-0.1344-0.0495-0.2508-0.22630.31010.3260.0132-0.1938-0.19010.2336-0.0470.03450.27320.01920.158235.0472-22.4664-24.9657
81.75450.1987-0.49262.5375-1.51852.7502-0.06960.0581-0.0573-0.03530.0690.1531-0.0359-0.0732-0.00920.20260.0599-0.02980.2455-0.0480.163127.9497-22.2539-12.583
91.514-0.1033-1.37751.3427-0.84072.80410.07470.12730.08930.10610.0814-0.044-0.5868-0.3803-0.17950.39970.0577-0.05530.2770.03350.197734.5363-6.08-37.1003
105.8751-5.3175-0.15496.81510.84213.5169-0.0235-0.21440.63770.14220.2332-0.8214-0.21220.3972-0.22030.2512-0.03140.02960.284-0.01330.210643.673-16.8598-32.6238
115.4421-0.6374-2.9173.5241-1.80485.5073-0.19550.1147-0.2275-0.32690.07530.39610.0731-0.26560.10350.2685-0.0164-0.00850.2073-0.02680.14938.5679-15.6501-43.323
123.3534-0.5103-0.21132.82580.8511.77650.07130.0083-0.06850.07260.0839-0.113-0.27970.1078-0.16990.38040.0239-0.03630.24580.01210.129848.6353-5.6775-46.3586
133.4708-1.8534-1.6422.23641.71393.14910.0631-0.3484-0.23130.32350.1321-0.98590.18840.5994-0.19290.302-0.0186-0.11860.5725-0.02310.8318-4.2254-25.8898-22.222
146.0895-0.19710.12541.7312-0.57930.81720.36490.09780.4243-0.1578-0.2457-0.55420.11240.0744-0.0940.2530.0083-0.03730.4680.0240.3631-18.0097-27.035-26.0473
150.773-1.1843-0.15043.13521.41844.72850.29640.19550.17850.36530.1571-0.04260.5165-0.0204-0.41540.2842-0.1168-0.13410.4380.01290.5349-15.0163-28.8828-16.3876
162.8323-0.6752-1.10425.76820.88133.06970.2740.18130.0920.8742-0.2775-0.486-0.1957-0.14-0.01160.433-0.0436-0.11210.36660.03180.4097-11.9963-18.0844-13.1791
173.30650.5035-0.61250.14230.2130.88210.00860.3901-0.893-0.0648-0.0041-1.12810.13040.2959-0.03160.35160.03910.03220.607500.8867-4.3867-36.2844-36.8501
184.40660.6671-2.25443.7098-0.1244.9287-0.16380.7183-0.0647-0.49430.1783-0.43630.2057-0.02420.00270.29390.05920.02820.4911-0.05960.4163-17.069-35.5467-39.4529
196.30740.94140.18090.6382-0.61950.9718-0.09390.855-1.1614-0.36980.3874-0.74030.36990.1293-0.18950.5519-0.01370.29930.8584-0.24631.1233-11.0121-48.1511-47.0867
203.1306-2.00011.81181.9718-0.88851.63190.26880.2634-1.0091-0.0523-0.09490.89670.4272-0.1593-0.15090.5437-0.0656-0.04860.3269-0.08920.6278-9.960512.3037-35.1481
212.3285-0.18070.30532.6745-0.99891.7375-0.09240.1864-0.1862-0.08430.2950.2690.0408-0.1773-0.18870.4094-0.00510.02350.304-0.04190.3828-8.20525.4446-38.738
222.09480.5187-1.15957.2841-0.35990.67160.60310.2506-0.8799-0.5302-0.1080.40940.5837-0.1031-0.50690.7144-0.1787-0.22680.5529-0.14920.7522-17.752611.9252-44.944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 11 through 21 )C11 - 21
2X-RAY DIFFRACTION2chain 'C' and (resid 22 through 51 )C22 - 51
3X-RAY DIFFRACTION3chain 'C' and (resid 52 through 96 )C52 - 96
4X-RAY DIFFRACTION4chain 'C' and (resid 97 through 183 )C97 - 183
5X-RAY DIFFRACTION5chain 'C' and (resid 184 through 203 )C184 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 11 through 51 )A11 - 51
7X-RAY DIFFRACTION7chain 'A' and (resid 52 through 95 )A52 - 95
8X-RAY DIFFRACTION8chain 'A' and (resid 96 through 203 )A96 - 203
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 52 )B11 - 52
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 95 )B53 - 95
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 134 )B96 - 134
12X-RAY DIFFRACTION12chain 'B' and (resid 135 through 203 )B135 - 203
13X-RAY DIFFRACTION13chain 'D' and (resid 11 through 51 )D11 - 51
14X-RAY DIFFRACTION14chain 'D' and (resid 52 through 95 )D52 - 95
15X-RAY DIFFRACTION15chain 'D' and (resid 96 through 120 )D96 - 120
16X-RAY DIFFRACTION16chain 'D' and (resid 121 through 203 )D121 - 203
17X-RAY DIFFRACTION17chain 'E' and (resid 11 through 64 )E11 - 64
18X-RAY DIFFRACTION18chain 'E' and (resid 65 through 134 )E65 - 134
19X-RAY DIFFRACTION19chain 'E' and (resid 135 through 202 )E135 - 202
20X-RAY DIFFRACTION20chain 'F' and (resid 11 through 51 )F11 - 51
21X-RAY DIFFRACTION21chain 'F' and (resid 52 through 174 )F52 - 174
22X-RAY DIFFRACTION22chain 'F' and (resid 175 through 203 )F175 - 203

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