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- PDB-3jtw: Crystal structure of Putative dihydrofolate reductase (YP_805003.... -

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Basic information

Entry
Database: PDB / ID: 3jtw
TitleCrystal structure of Putative dihydrofolate reductase (YP_805003.1) from PEDIOCOCCUS PENTOSACEUS ATCC 25745 at 1.90 A resolution
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / YP_805003.1 / Putative dihydrofolate reductase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / RibD C-terminal domain
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process
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
Unknown ligand / Dihydrofolate reductase
Similarity search - Component
Biological speciesPediococcus pentosaceus ATCC 25745 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative dihydrofolate reductase (YP_805003.1) from PEDIOCOCCUS PENTOSACEUS ATCC 25745 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9358
Polymers41,4882
Non-polymers4466
Water3,729207
1
A: Dihydrofolate reductase
hetero molecules

A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,99710
Polymers41,4882
Non-polymers5088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5400 Å2
ΔGint-78 kcal/mol
Surface area16970 Å2
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules

B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8726
Polymers41,4882
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4030 Å2
ΔGint-74 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.759, 83.314, 65.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 23
2114B2 - 23
1126A24 - 30
2126B24 - 30
1134A31 - 177
2134B31 - 177

NCS ensembles :
ID
1
2
3
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Dihydrofolate reductase


Mass: 20744.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus ATCC 25745 (bacteria)
Strain: ATCC 25745 / 183-1w / Gene: PEPE_1533, YP_805003.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q03E11
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. 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. 2. THE ELECTRON DENSITY AT POSITION 120 SUPPORTS THE ASSIGNMENT AS ISOLEUCINE AND NOT LEUCINE. DNA SEQUENCING OF THE CLONED CONSTRUCT GAVE VERY CLEAN READS EXCEPT FOR THE FIRST POSITION OF THE RESIDUE 120 CODON, WHICH GAVE TWO PEAKS CORRESPONDING TO ATT (ISOLEUCINE) AND CTT (LEUCINE).

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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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 2.0000M (NH4)2SO4, 5.0000% iso-Propanol, 0.1M Citrate pH 4.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.91162,0.97943,0.97959
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2009
Details: Flat mirror, vertical and horizontal focussing mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979431
30.979591
ReflectionResolution: 1.9→29.476 Å / Num. obs: 30501 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 20.63 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.9540.5981.2891022270.598100
1.95-240.5541.1871721710.554100
2-2.0640.4151.8848521060.415100
2.06-2.1240.3582829720610.358100
2.12-2.1940.3042.5798419820.304100
2.19-2.2740.2862.5781919390.286100
2.27-2.3640.2512.6741818540.251100
2.36-2.4540.2053.6730018100.205100
2.45-2.5640.1923.8689517120.192100
2.56-2.6940.1684.5669316640.16899.9
2.69-2.834.10.135.6637815730.1399.9
2.83-340.0987.2601215040.09899.9
3-3.2140.0858.3564614050.08599.8
3.21-3.4740.06510525813080.06599.8
3.47-3.840.05312.2486112110.05399.6
3.8-4.2540.04513.7441411060.04599.5
4.25-4.913.90.05111.138779820.05199.4
4.91-6.013.90.05410.633158460.05498.9
6.01-8.53.80.04314.525126570.04398.7
8.5-29.483.50.03716.313513830.03795.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.476 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.527 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.145
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). 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. (4). RESIDUES 64-67 OF B CHAIN ARE DISORDERED AND ELECTRON DENSITIES ARE POOR IN THIS REGION. THEY ARE NOT MODELED. (5). SULFATE (SO4) IONS FROM THE CRYSTALLIZATION BUFFERS AND ETHYLENE GLYCOL (EDO) FROM THE CRYO SOLUTIONS WERE MODELED INTO THE STRUCTURE. (6) THERE IS UNIDENTIFIED DENSITY FOUND NEAR THE PUTATIVE ACTIVE SITE OF A CHAIN. IT WAS MODELED AS AN UNKNOWN LIGAND (UNL).
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1539 5 %RANDOM
Rwork0.182 ---
obs0.184 30477 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.41 Å2 / Biso mean: 26.844 Å2 / Biso min: 9.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--1.59 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 33 207 3054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223082
X-RAY DIFFRACTIONr_bond_other_d0.0010.022050
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9634209
X-RAY DIFFRACTIONr_angle_other_deg0.96635036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68124.685143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28715561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0181517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023463
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02612
X-RAY DIFFRACTIONr_nbd_refined0.1970.2545
X-RAY DIFFRACTIONr_nbd_other0.1910.22176
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21517
X-RAY DIFFRACTIONr_nbtor_other0.0880.21661
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.2121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.235
X-RAY DIFFRACTIONr_mcbond_it2.03232044
X-RAY DIFFRACTIONr_mcbond_other0.683745
X-RAY DIFFRACTIONr_mcangle_it2.64343042
X-RAY DIFFRACTIONr_scbond_it3.40251379
X-RAY DIFFRACTIONr_scangle_it4.44561167
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1273MEDIUM POSITIONAL0.190.5
1273MEDIUM THERMAL1.062
298LOOSE POSITIONAL1.425
298LOOSE THERMAL4.9310
31967MEDIUM POSITIONAL0.280.5
31967MEDIUM THERMAL1.082
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 121 -
Rwork0.241 2105 -
all-2226 -
obs--100 %
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)
10.4895-0.3992-0.16720.9035-0.13760.3340.01550.02540.0440.02460.00160.0158-0.0722-0.134-0.0171-0.06830.022-0.0077-0.0455-0.001-0.047128.117714.210336.585
21.11220.1465-0.04971.05220.84091.773-0.0271-0.0933-0.11640.10990.1414-0.17730.22630.3632-0.11430.02790.0504-0.00730.0350-0.024714.066235.098561.0992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 177
2X-RAY DIFFRACTION2B2 - 177

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