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- PDB-3mbj: Crystal structure of a putative phosphomethylpyrimidine kinase (B... -

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Basic information

Entry
Database: PDB / ID: 3mbj
TitleCrystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)
ComponentsPutative phosphomethylpyrimidine kinase
KeywordsTRANSFERASE / Putative phosphomethylpyrimidine kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Kinase
Function / homology
Function and homology information


pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / metal ion binding / cytosol
Similarity search - Function
Pyridoxine kinase / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / pyridoxal kinase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / pdbx_struct_conn_angle ...database_2 / 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
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,39812
Polymers33,4331
Non-polymers96611
Water2,234124
1
A: Putative phosphomethylpyrimidine kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)206,38972
Polymers200,5956
Non-polymers5,79466
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area33700 Å2
ΔGint-784 kcal/mol
Surface area57120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.627, 161.627, 76.138
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-291-

ZN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative phosphomethylpyrimidine kinase / Pyridoxine kinase


Mass: 33432.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_4458 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q89ZB9

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Non-polymers , 7 types, 135 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 35.00% 2-methyl-2,4-pentanediol, 0.20M lithium sulfate, 0.1M MES pH 6.0, Additive: 0.001M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97916,0.97871
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979161
30.978711
ReflectionResolution: 2.1→29.591 Å / Num. obs: 22278 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 28.253 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.155.70.8380.9934616450.838100
2.15-2.215.70.7031.1899315820.703100
2.21-2.285.70.5661.2876315370.566100
2.28-2.355.70.5141.5854115040.514100
2.35-2.425.70.4321.8840714780.432100
2.42-2.515.70.3852809914150.385100
2.51-2.65.70.3242.3769813510.324100
2.6-2.715.70.2682.8753813210.268100
2.71-2.835.70.2313.3721412650.231100
2.83-2.975.70.1784.2689312090.178100
2.97-3.135.70.1445.1661611600.144100
3.13-3.325.70.1156.2619710900.115100
3.32-3.555.70.0977578810150.097100
3.55-3.835.70.0887.354549650.088100
3.83-4.25.60.0797.849658840.079100
4.2-4.75.60.0698.744457960.069100
4.7-5.425.60.0728.539867160.072100
5.42-6.645.50.0798.233516050.079100
6.64-9.395.40.0629.325654740.062100
9.39-29.595.10.0638.713552660.06396.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.591 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 9.557 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.154
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 PROTEIN ...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. SULFATE IONS (SO4) AND 2-METHYL-2,4-PENTANEDIOL (MPD & MRD) MOLECULES FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE. 5. AN IMIDAZOLE MOLECULE (IMD) FROM THE PROTEIN BUFFER IS MODELED IN THIS STRUCTURE. 6. ZINC IONS (ZN) AND A CHLORIDE ANION (CL) FROM THE CRYSTALLIZATION DROP ADDITIVE ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1137 5.1 %RANDOM
Rwork0.171 ---
obs0.173 22278 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.3 Å2 / Biso mean: 23.496 Å2 / Biso min: 3.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å2-0.89 Å20 Å2
2---1.79 Å20 Å2
3---2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 51 124 2432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222410
X-RAY DIFFRACTIONr_bond_other_d0.0010.021591
X-RAY DIFFRACTIONr_angle_refined_deg1.61523290
X-RAY DIFFRACTIONr_angle_other_deg0.94133907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37424.43397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49715403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5431510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
X-RAY DIFFRACTIONr_mcbond_it0.7591.51480
X-RAY DIFFRACTIONr_mcbond_other0.1941.5590
X-RAY DIFFRACTIONr_mcangle_it1.39622414
X-RAY DIFFRACTIONr_scbond_it2.4883930
X-RAY DIFFRACTIONr_scangle_it3.6984.5876
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 91 -
Rwork0.249 1545 -
all-1636 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -5.4084 Å / Origin y: 25.2169 Å / Origin z: -14.0687 Å
111213212223313233
T0.134 Å20.0026 Å2-0.0168 Å2-0.1053 Å20.0719 Å2--0.1035 Å2
L0.9364 °20.2012 °2-0.1087 °2-1.2428 °20.0075 °2--0.2168 °2
S-0.0417 Å °0.1772 Å °0.2666 Å °-0.1791 Å °0.0428 Å °0.1118 Å °-0.0522 Å °-0.0065 Å °-0.0011 Å °

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