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- PDB-4odj: Crystal structure of a putative S-adenosylmethionine synthetase f... -

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Entry
Database: PDB / ID: 4odj
TitleCrystal structure of a putative S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with S-adenosyl-methionine
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / SSGCID / Cryptosporidium hominis / S-adenosylmethionine synthase / S-adenosyl-L-methionine / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyGMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / TRIPHOSPHATE / S-ADENOSYLMETHIONINE / :
Function and homology information
Biological speciesCryptosporidium hominis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a putative S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with S-adenosyl-methionine
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Arakaki, T. / Lorimer, D. / Edewars, T.E.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6605
Polymers45,9551
Non-polymers7054
Water5,350297
1
A: S-adenosylmethionine synthase
hetero molecules

A: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,32110
Polymers91,9112
Non-polymers1,4108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area7690 Å2
ΔGint-75 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.860, 117.860, 54.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

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Components

#1: Protein S-adenosylmethionine synthase


Mass: 45955.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Gene: Chro.70301 / Plasmid: CrhoA.00729.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5CKX0, methionine adenosyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Microlytics MCSG1 screen, g11: 100mM Na2HPO4/citric acid pH 4.2, 40% PEG 300; CrhoA.00729.a.B1.PW37315 at 28.4mg/ml + 2.5mM S-Adenosyl-Methionine; tray 247830, puck QJI2-2, VAPOR DIFFUSION, ...Details: Microlytics MCSG1 screen, g11: 100mM Na2HPO4/citric acid pH 4.2, 40% PEG 300; CrhoA.00729.a.B1.PW37315 at 28.4mg/ml + 2.5mM S-Adenosyl-Methionine; tray 247830, puck QJI2-2, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 16, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 57078 / Num. obs: 56815 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.262 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.640.562.39154184175199.5
1.64-1.690.4363.08150554061199.7
1.69-1.740.3623.62145053923199.6
1.74-1.790.3124.26143183858199.6
1.79-1.850.2435.5137993711199.6
1.85-1.910.1976.65133903599199.6
1.91-1.980.158.54129863485199.7
1.98-2.070.12410.25126013398199.7
2.07-2.160.09513.09120483231199.7
2.16-2.260.07615.48113743056199.5
2.26-2.390.06617.7108932933199.6
2.39-2.530.05720.11102992790199.7
2.53-2.70.0522.6896952647199.7
2.7-2.920.04325.388042416199.8
2.92-3.20.03728.7183172281199.8
3.2-3.580.03333.4773122034199.4
3.58-4.130.02836.9864681803199.2
4.13-5.060.02639.4454831525199
5.06-7.160.02638.4443721221199.8
7.16-500.02538.952168668194.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.91 Å
Translation3.5 Å19.91 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SO4 modified with CCP4 program chainsaw

3so4


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1558 / WRfactor Rwork: 0.1365 / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8879 / SU B: 2.816 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0681 / SU Rfree: 0.0674 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1652 2803 4.9 %RANDOM
Rwork0.1445 ---
obs0.1456 56815 99.53 %-
all-57078 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.37 Å2 / Biso mean: 20.8199 Å2 / Biso min: 7.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 42 297 3273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193158
X-RAY DIFFRACTIONr_bond_other_d0.0010.023028
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.984316
X-RAY DIFFRACTIONr_angle_other_deg0.82436997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57624.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1415550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4761516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
X-RAY DIFFRACTIONr_mcbond_it0.8451.0851590
X-RAY DIFFRACTIONr_mcbond_other0.8451.0851590
X-RAY DIFFRACTIONr_mcangle_it1.3921.6251995
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 171 -
Rwork0.226 3992 -
all-4163 -
obs-4175 99.5 %
Refinement TLS params.Method: refined / Origin x: 87.988 Å / Origin y: 50.882 Å / Origin z: 2.501 Å
111213212223313233
T0.0798 Å2-0.0282 Å20.0024 Å2-0.0335 Å20.0006 Å2--0.057 Å2
L1.3562 °20.4733 °2-0.1952 °2-0.46 °2-0.0548 °2--0.2662 °2
S0.18 Å °-0.1297 Å °0.013 Å °0.1776 Å °-0.0982 Å °-0.0003 Å °-0.0608 Å °-0.0118 Å °-0.0818 Å °

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