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- PDB-2gd9: Crystal structure of a putative dihydrofolate reductase (bsu40760... -

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Basic information

Entry
Database: PDB / ID: 2gd9
TitleCrystal structure of a putative dihydrofolate reductase (bsu40760, yyap) from bacillus subtilis at 2.30 A resolution
ComponentsHypothetical protein yyaPHypothesis
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / membrane => GO:0016020
Similarity search - Function
Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized protein YyaP
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (2636623) from BACILLUS SUBTILIS at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein yyaP
B: Hypothetical protein yyaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4899
Polymers44,0152
Non-polymers4747
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-31 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.915, 64.915, 143.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYLYSAA0 - 551 - 56
21GLYLYSBB0 - 551 - 56
12LYSTYRAA74 - 8675 - 87
22LYSTYRBB74 - 8675 - 87
13ILETRPAA106 - 186107 - 187
23ILEASNBB106 - 187107 - 188

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Hypothetical protein yyaP / Hypothesis


Mass: 22007.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yyaP / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: P37508
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.57 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.9
Details: 0.2M (NH4)2HPO4, 20.0% PEG-3350, No Buffer pH 7.9, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.019859, 0.979718
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0198591
20.9797181
ReflectionResolution: 2.3→64.957 Å / Num. obs: 26393 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value
2.3-2.361003.70.7471719219250.747
2.36-2.421003.70.671.1709219020.67
2.42-2.491003.70.5961.2696118610.596
2.49-2.571003.80.5641.3666917750.564
2.57-2.661003.80.4161.8646517240.416
2.66-2.751003.70.3422.1634016950.342
2.75-2.851003.70.2842.6608116220.284
2.85-2.971003.70.1953.8587815720.195
2.97-3.11003.70.1624.5561614990.162
3.1-3.251003.80.1216.1537914320.121
3.25-3.431003.80.0927.9514313700.092
3.43-3.641003.70.0769.1480612830.076
3.64-3.891003.70.06710.5450812040.067
3.89-4.21003.70.0549.5421611320.054
4.2-4.61003.70.04216.1390110440.042
4.6-5.141003.70.03819.234889450.038
5.14-5.941003.70.04316.230868350.043
5.94-7.271003.70.04814.926327140.048
7.27-10.291003.60.02625.719865510.026
10.29-64.9698.43.30.0229.710183080.02

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→59.16 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.184 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES 63-74 OF BOTH CHAINS, AND 90-100 OF CHAIN B WERE DISORDERED AND NOT MODELED. 4. THE MAINCHAIN AND SIDECHAIN POSITIONS OF B186 WERE MODELED BASED ON THE POSITION OF THE A CHAIN. THE C-TERMINAL REGION OF BOTH MONOMERS LIES ON A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS, MAKING THE INTERPRETATION OF THE DISORDERED DENSITY IN THIS AREA PROBLEMATIC. 5. GLY125-126 IS IN THE CIS-CONFORMATION IN BOTH CHAINS. THIS IS LOCATED IN THE ACTIVE SITE AND IS CONSERVED IN OTHER DIHYDROFOLATE REDUCTAESES. 6. PO4 AND CL ARE MODELED IN THE PUTATIVE ACTIVE SITE. 7. EDO MODELED BASED ON CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1364 5.2 %RANDOM
Rwork0.207 ---
all0.21 ---
obs0.20966 26334 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.972 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 27 155 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222927
X-RAY DIFFRACTIONr_bond_other_d0.0010.022688
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9483949
X-RAY DIFFRACTIONr_angle_other_deg0.85536244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.17924.71138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37315531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5221513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02596
X-RAY DIFFRACTIONr_nbd_refined0.1640.2455
X-RAY DIFFRACTIONr_nbd_other0.1810.22620
X-RAY DIFFRACTIONr_nbtor_refined0.170.21325
X-RAY DIFFRACTIONr_nbtor_other0.0840.21724
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.215
X-RAY DIFFRACTIONr_mcbond_it0.7081.51777
X-RAY DIFFRACTIONr_mcbond_other0.1261.5722
X-RAY DIFFRACTIONr_mcangle_it1.1722790
X-RAY DIFFRACTIONr_scbond_it1.60731342
X-RAY DIFFRACTIONr_scangle_it2.4834.51157
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1328MEDIUM POSITIONAL0.130.5
1521LOOSE POSITIONAL0.545
1328MEDIUM THERMAL0.452
1521LOOSE THERMAL0.9710
278MEDIUM POSITIONAL0.220.5
2146LOOSE POSITIONAL0.815
278MEDIUM THERMAL0.962
2146LOOSE THERMAL1.9510
3472MEDIUM POSITIONAL0.160.5
3768LOOSE POSITIONAL0.455
3472MEDIUM THERMAL0.692
3768LOOSE THERMAL1.0910
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 95 -
Rwork0.275 1824 -
obs-1919 99.69 %
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)
11.1127-0.1111-0.18910.4902-0.06552.27740.01220.0528-0.064-0.02630.02760.05850.2152-0.2131-0.0397-0.0571-0.05380.0058-0.0049-0.0036-0.062817.232628.083483.681
20.50830.3384-0.40541.5452-0.70352.5250.0562-0.03760.09970.01510.02810.1701-0.293-0.1067-0.08430.00170.0221-0.0094-0.09030.0033-0.048828.3747.001559.8926
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 186 / Label seq-ID: 1 - 187

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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