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- PDB-1vly: Crystal structure of a putative aminomethyltransferase (ygfz) fro... -

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Basic information

Entry
Database: PDB / ID: 1vly
TitleCrystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution
ComponentsUnknown protein from 2D-page
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


RNA modification / tRNA processing / iron-sulfur cluster assembly / folic acid binding / cytosol / cytoplasm
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #160 / Alpha-Beta Plaits - #1630 / tRNA-modifying protein YgfZ / : / YgfZ, beta-barrel domain / YgfZ/GcvT conserved site / YgfZ/GcvT / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein/YgfZ, C-terminal / Aminomethyltransferase, folate-binding domain ...Elongation Factor Tu (Ef-tu); domain 3 - #160 / Alpha-Beta Plaits - #1630 / tRNA-modifying protein YgfZ / : / YgfZ, beta-barrel domain / YgfZ/GcvT conserved site / YgfZ/GcvT / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein/YgfZ, C-terminal / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / tRNA-modifying protein YgfZ / tRNA-modifying protein YgfZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Unknown protein from 2D-page (Spot PR51) (b2898) from Escherichia coli k12 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 25, 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.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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Unknown protein from 2D-page
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4317
Polymers38,1101
Non-polymers3216
Water8,593477
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.814, 50.080, 52.014
Angle α, β, γ (deg.)94.68, 115.29, 116.46
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Unknown protein from 2D-page / Spot PR51


Mass: 38110.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygfZ, b2898 / Production host: Escherichia coli (E. coli) / References: UniProt: P39179, UniProt: P0ADE8*PLUS

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Non-polymers , 5 types, 483 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.1 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.3
Details: 0.2M CaAcetate, 20.0% PEG-3350, No Buffer pH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-110.979129
SYNCHROTRONSSRL BL11-120.979508,0.885567
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2004 / Details: flat mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791291
20.9795081
30.8855671
ReflectionResolution: 1.3→26.45 Å / Num. obs: 75749 / % possible obs: 89.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.89 Å2 / Rsym value: 0.036 / Net I/σ(I): 17.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 7630 / Rsym value: 0.339 / % possible all: 61.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHARPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.3→26.45 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.364 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.047
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 1. TWO CALCIUM CATIONS WERE TENTAIVELY MODELED INTO THE STRUCTURE BASED ON THE INCLUSION OF 0.2M CALCIUM ACETATE IN THE CRYSTALLIZATION, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 1. TWO CALCIUM CATIONS WERE TENTAIVELY MODELED INTO THE STRUCTURE BASED ON THE INCLUSION OF 0.2M CALCIUM ACETATE IN THE CRYSTALLIZATION, AND PROXIMITY OF THE TWO SITES TO NEGATIVELY-CHARGED AMINO ACID SIDECHAINS. THE BOND VALENCE (MULLER ET AL. ACTA CRYST D. 2003 D59 PP. 32-37) ALSO INDICATES ASSIGNING A CA+2 CATION AT THIS POSITION. 2. THE ELECTRON DENSITY BETWEEN RESIDUES A260-A264 AND A269-A272 IS WEAK, THEREFORE, IT WAS NOT POSSIBLE TO BUILD SIDECHAIN COORDINATES IN THIS REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.16785 3802 5 %RANDOM
Rwork0.13402 ---
obs0.13572 71946 89.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20.37 Å2-0.09 Å2
2---0.14 Å20.28 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 18 477 2970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222588
X-RAY DIFFRACTIONr_bond_other_d0.0010.022397
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9613510
X-RAY DIFFRACTIONr_angle_other_deg1.05235569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92724.696115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9415442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1081516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_nbd_refined0.2240.2462
X-RAY DIFFRACTIONr_nbd_other0.1920.22425
X-RAY DIFFRACTIONr_nbtor_other0.0850.21610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2377
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.235
X-RAY DIFFRACTIONr_mcbond_it2.42731682
X-RAY DIFFRACTIONr_mcbond_other1.4113656
X-RAY DIFFRACTIONr_mcangle_it3.17152613
X-RAY DIFFRACTIONr_scbond_it4.13581043
X-RAY DIFFRACTIONr_scangle_it5.37511897
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21261
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.25
X-RAY DIFFRACTIONr_rigid_bond_restr1.93835490
X-RAY DIFFRACTIONr_sphericity_free6.5063479
X-RAY DIFFRACTIONr_sphericity_bonded3.45234938
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 170 5.06 %
Rwork0.207 3189 -
obs--53.53 %

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