HEADER TRANSFERASE 27-FEB-09 3GGD TITLE CRYSTAL STRUCTURE OF SAM-DEPENDENT METHYLTRANSFERASE (YP_325210.1) TITLE 2 FROM ANABAENA VARIABILIS ATCC 29413 AT 2.11 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAM-DEPENDENT METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANABAENA VARIABILIS ATCC 29413; SOURCE 3 ORGANISM_TAXID: 240292; SOURCE 4 ATCC: 29413; SOURCE 5 GENE: AVA_4718, YP_325210.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS YP_325210.1, SAM-DEPENDENT METHYLTRANSFERASE, STRUCTURAL GENOMICS, KEYWDS 2 JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, PSI-2, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 16-OCT-24 3GGD 1 REMARK REVDAT 5 01-FEB-23 3GGD 1 REMARK SEQADV REVDAT 4 24-JUL-19 3GGD 1 REMARK LINK REVDAT 3 25-OCT-17 3GGD 1 REMARK REVDAT 2 13-JUL-11 3GGD 1 VERSN REVDAT 1 31-MAR-09 3GGD 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF SAM-DEPENDENT METHYLTRANSFERASE JRNL TITL 2 (YP_325210.1) FROM ANABAENA VARIABILIS ATCC 29413 AT 2.11 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 42037 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2128 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2863 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 177 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 40.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : -1.89000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.175 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2116 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1424 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2875 ; 1.646 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3471 ; 0.947 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 258 ; 5.251 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;30.854 ;24.348 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 330 ;11.287 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;15.286 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 313 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2342 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 428 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 425 ; 0.216 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1545 ; 0.204 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1001 ; 0.187 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 969 ; 0.089 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 293 ; 0.180 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.043 ; 0.500 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.288 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 36 ; 0.184 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.210 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1326 ; 0.923 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 505 ; 0.217 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2048 ; 1.302 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 937 ; 2.301 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 827 ; 3.204 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 244 REMARK 3 ORIGIN FOR THE GROUP (A): 12.5878 41.0960 7.2816 REMARK 3 T TENSOR REMARK 3 T11: -0.1710 T22: -0.1496 REMARK 3 T33: -0.1760 T12: 0.0016 REMARK 3 T13: -0.0059 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.7105 L22: 1.9002 REMARK 3 L33: 1.4240 L12: -0.0314 REMARK 3 L13: -0.3779 L23: 0.8043 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: -0.0891 S13: -0.2023 REMARK 3 S21: 0.0267 S22: -0.0809 S23: -0.0527 REMARK 3 S31: 0.0870 S32: -0.0175 S33: 0.0867 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS REMARK 3 ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REMARK 3 REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.S- REMARK 3 ADENOSYLMETHIONINE WAS ADDED DURING CRYSTALLIZATION. IN THIS REMARK 3 STRUCTURE, ONLY S-ADENOSYL-L-HOMOCYSTEINE( SAH) IS MODELED IN REMARK 3 THE CONSERVED BINDING SITE DUE TO A POSSIBLE ENZYMATICALLY REMARK 3 RELATED DEGRADATION. AN UNKNOWN LIGAND (UNL) IS MODELED NEXT TO REMARK 3 THE S-ADENOSYL-L- HOMOCYSTEINE IN THE SAME BINDING SITE. THE REMARK 3 SHAPE OF THE LIGAND IS CREATINE LIKE. 5.A COBALT ION FROM THE REMARK 3 CRYSTALLIZATION REAGENT IS MODELED IN THIS STRUCTURE. THE REMARK 3 PRESENCE OF THE CO ATOM IS SUPPORTED BY X-RAY FLUORESCENCE REMARK 3 MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. REMARK 3 ADDITIONAL ELECTRON DENSITY IS OBSERVED ADJACENT TO THE COBALT REMARK 3 ION AND NEAR TO RESIDUES 203 AND 243. THIS DENSITY WAS LEFT REMARK 3 UNMODELED. 6.AN IMIDAZOLE MOLECULE AND CHLORIDE ION FROM THE REMARK 3 PROTEIN BUFFER, SULFATE IONS FROM THE CRYSTALLIZATION CONDITION REMARK 3 AND ETHYLENE GLYCOL MOLECULES FROM THE CRYOPROTECTANT ARE ALSO REMARK 3 MODELED IN THIS STRUCTURE. REMARK 4 REMARK 4 3GGD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94645,0.97967 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMETER REMARK 200 OPTICS : ADJUSTABLE FOCUSING MIRRORS IN K REMARK 200 -B GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42096 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 30.083 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 17.90 REMARK 200 R MERGE (I) : 0.22100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS REMARK 200 SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND . REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M COBALT CHLORIDE, 1.8M AMMONIUM REMARK 280 SULFATE, 0.1M MES PH 6.5, ADDITIVE: 0.001 M S-ADENOSYLMETHIONINE REMARK 280 (SAM), NANODROP', VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.28000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 56.26000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.14000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.26000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 56.26000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 84.42000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.26000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.26000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.14000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 56.26000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.26000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 84.42000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.28000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE REMARK 300 ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 MSE A 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 LYS A 3 NZ REMARK 470 ILE A 7 CG1 CG2 CD1 REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 LYS A 95 CE NZ REMARK 470 GLU A 113 CD OE1 OE2 REMARK 470 GLU A 176 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 183 CZ TYR A 183 OH 0.103 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 7 -72.98 -85.97 REMARK 500 ALA A 41 -104.15 -127.86 REMARK 500 ASN A 97 48.78 -140.53 REMARK 500 GLU A 217 -98.79 -124.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 246 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 209 OD2 REMARK 620 2 HIS A 243 NE2 109.7 REMARK 620 3 IMD A 249 N1 109.5 110.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL A 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 251 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 253 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 254 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 255 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 256 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 257 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 262 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 379018 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3GGD A 1 244 UNP Q3M3X1 Q3M3X1_ANAVT 1 244 SEQADV 3GGD GLY A 0 UNP Q3M3X1 EXPRESSION TAG SEQRES 1 A 245 GLY MSE GLU LYS LEU SER ALA ILE LYS LYS PRO ASP ILE SEQRES 2 A 245 ASN VAL ALA ASP ALA TRP GLU GLN TYR TRP ASN LYS THR SEQRES 3 A 245 LEU VAL ASN SER THR PRO VAL LEU TRP ASP ALA ASN VAL SEQRES 4 A 245 GLU ARG ALA VAL VAL VAL ASP LEU PRO ARG PHE GLU LEU SEQRES 5 A 245 LEU PHE ASN PRO GLU LEU PRO LEU ILE ASP PHE ALA CYS SEQRES 6 A 245 GLY ASN GLY THR GLN THR LYS PHE LEU SER GLN PHE PHE SEQRES 7 A 245 PRO ARG VAL ILE GLY LEU ASP VAL SER LYS SER ALA LEU SEQRES 8 A 245 GLU ILE ALA ALA LYS GLU ASN THR ALA ALA ASN ILE SER SEQRES 9 A 245 TYR ARG LEU LEU ASP GLY LEU VAL PRO GLU GLN ALA ALA SEQRES 10 A 245 GLN ILE HIS SER GLU ILE GLY ASP ALA ASN ILE TYR MSE SEQRES 11 A 245 ARG THR GLY PHE HIS HIS ILE PRO VAL GLU LYS ARG GLU SEQRES 12 A 245 LEU LEU GLY GLN SER LEU ARG ILE LEU LEU GLY LYS GLN SEQRES 13 A 245 GLY ALA MSE TYR LEU ILE GLU LEU GLY THR GLY CYS ILE SEQRES 14 A 245 ASP PHE PHE ASN SER LEU LEU GLU LYS TYR GLY GLN LEU SEQRES 15 A 245 PRO TYR GLU LEU LEU LEU VAL MSE GLU HIS GLY ILE ARG SEQRES 16 A 245 PRO GLY ILE PHE THR ALA GLU ASP ILE GLU LEU TYR PHE SEQRES 17 A 245 PRO ASP PHE GLU ILE LEU SER GLN GLY GLU GLY LEU PHE SEQRES 18 A 245 GLN SER ILE HIS LYS LEU PRO ASP GLY ASN TYR ALA THR SEQRES 19 A 245 PRO PRO ALA PHE TRP ALA VAL ILE LYS HIS ARG MODRES 3GGD MSE A 129 MET SELENOMETHIONINE MODRES 3GGD MSE A 158 MET SELENOMETHIONINE MODRES 3GGD MSE A 189 MET SELENOMETHIONINE HET MSE A 129 8 HET MSE A 158 8 HET MSE A 189 8 HET UNL A 245 9 HET CO A 246 1 HET CL A 247 1 HET SAH A 248 26 HET IMD A 249 5 HET SO4 A 250 5 HET SO4 A 251 5 HET SO4 A 252 5 HET SO4 A 253 5 HET EDO A 254 4 HET EDO A 255 4 HET EDO A 256 4 HET EDO A 257 4 HET EDO A 258 4 HET EDO A 259 4 HET EDO A 260 4 HET EDO A 261 4 HET EDO A 262 4 HETNAM MSE SELENOMETHIONINE HETNAM UNL UNKNOWN LIGAND HETNAM CO COBALT (II) ION HETNAM CL CHLORIDE ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM IMD IMIDAZOLE HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 3 CO CO 2+ FORMUL 4 CL CL 1- FORMUL 5 SAH C14 H20 N6 O5 S FORMUL 6 IMD C3 H5 N2 1+ FORMUL 7 SO4 4(O4 S 2-) FORMUL 11 EDO 9(C2 H6 O2) FORMUL 20 HOH *192(H2 O) HELIX 1 1 ASN A 13 SER A 29 1 17 HELIX 2 2 ASN A 37 ARG A 40 5 4 HELIX 3 3 ALA A 41 GLU A 50 1 10 HELIX 4 4 GLY A 67 PHE A 77 1 11 HELIX 5 5 SER A 86 ASN A 97 1 12 HELIX 6 6 VAL A 111 GLY A 123 1 13 HELIX 7 7 PRO A 137 GLU A 139 5 3 HELIX 8 8 LYS A 140 GLY A 153 1 14 HELIX 9 9 GLY A 166 GLY A 179 1 14 HELIX 10 10 PRO A 182 GLU A 190 1 9 HELIX 11 11 THR A 199 PHE A 207 1 9 SHEET 1 A 7 ILE A 102 LEU A 106 0 SHEET 2 A 7 VAL A 80 ASP A 84 1 N GLY A 82 O SER A 103 SHEET 3 A 7 LEU A 59 PHE A 62 1 N ASP A 61 O ILE A 81 SHEET 4 A 7 ASN A 126 ARG A 130 1 O TYR A 128 N ILE A 60 SHEET 5 A 7 ALA A 157 LEU A 163 1 O TYR A 159 N ILE A 127 SHEET 6 A 7 ALA A 236 HIS A 243 -1 O PHE A 237 N GLU A 162 SHEET 7 A 7 PHE A 210 GLY A 216 -1 N GLU A 211 O LYS A 242 LINK C TYR A 128 N MSE A 129 1555 1555 1.33 LINK C MSE A 129 N ARG A 130 1555 1555 1.33 LINK C ALA A 157 N MSE A 158 1555 1555 1.34 LINK C MSE A 158 N TYR A 159 1555 1555 1.33 LINK C AVAL A 188 N MSE A 189 1555 1555 1.33 LINK C BVAL A 188 N MSE A 189 1555 1555 1.33 LINK C MSE A 189 N GLU A 190 1555 1555 1.32 LINK OD2 ASP A 209 CO CO A 246 1555 1555 2.02 LINK NE2 HIS A 243 CO CO A 246 1555 1555 2.05 LINK CO CO A 246 N1 IMD A 249 1555 1555 2.13 SITE 1 AC1 5 TRP A 34 THR A 131 HIS A 134 HIS A 135 SITE 2 AC1 5 PRO A 195 SITE 1 AC2 4 GLU A 50 ASP A 209 HIS A 243 IMD A 249 SITE 1 AC3 3 VAL A 14 LYS A 140 HOH A 319 SITE 1 AC4 18 VAL A 14 TRP A 18 TRP A 22 TRP A 34 SITE 2 AC4 18 ALA A 63 GLY A 65 ASP A 84 VAL A 85 SITE 3 AC4 18 LEU A 107 ASP A 108 GLY A 109 ARG A 130 SITE 4 AC4 18 THR A 131 HIS A 135 HOH A 263 HOH A 265 SITE 5 AC4 18 HOH A 266 HOH A 280 SITE 1 AC5 9 VAL A 43 LEU A 46 PRO A 47 GLU A 50 SITE 2 AC5 9 ARG A 149 ASP A 209 HIS A 243 CO A 246 SITE 3 AC5 9 HOH A 268 SITE 1 AC6 7 THR A 165 GLY A 166 CYS A 167 ILE A 168 SITE 2 AC6 7 ASP A 169 ILE A 197 HOH A 434 SITE 1 AC7 5 ARG A 79 SER A 103 ARG A 105 ILE A 118 SITE 2 AC7 5 HOH A 422 SITE 1 AC8 5 LYS A 154 GLN A 155 LYS A 242 HOH A 390 SITE 2 AC8 5 HOH A 401 SITE 1 AC9 3 ARG A 48 EDO A 261 HOH A 288 SITE 1 BC1 4 ASP A 35 ASN A 37 THR A 68 HOH A 278 SITE 1 BC2 6 ARG A 40 ALA A 41 ASP A 45 ARG A 130 SITE 2 BC2 6 ILE A 161 GLN A 221 SITE 1 BC3 6 VAL A 43 VAL A 44 PRO A 47 GLN A 146 SITE 2 BC3 6 ARG A 149 HOH A 310 SITE 1 BC4 8 GLN A 75 ASP A 124 GLY A 153 LYS A 154 SITE 2 BC4 8 GLN A 155 EDO A 260 HOH A 300 HOH A 329 SITE 1 BC5 4 GLU A 211 ILE A 212 HOH A 306 HOH A 402 SITE 1 BC6 5 TYR A 178 GLN A 180 PRO A 182 HIS A 224 SITE 2 BC6 5 PRO A 227 SITE 1 BC7 5 GLY A 123 ASP A 124 GLN A 155 EDO A 257 SITE 2 BC7 5 HOH A 282 SITE 1 BC8 6 ARG A 48 GLU A 217 GLY A 218 TRP A 238 SITE 2 BC8 6 SO4 A 253 HOH A 360 SITE 1 BC9 4 ARG A 105 LEU A 106 GLN A 114 GLN A 117 CRYST1 112.520 112.520 112.560 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008887 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008884 0.00000 CONECT 994 1004 CONECT 1004 994 1005 CONECT 1005 1004 1006 1008 CONECT 1006 1005 1007 1012 CONECT 1007 1006 CONECT 1008 1005 1009 CONECT 1009 1008 1010 CONECT 1010 1009 1011 CONECT 1011 1010 CONECT 1012 1006 CONECT 1231 1234 CONECT 1234 1231 1235 CONECT 1235 1234 1236 1238 CONECT 1236 1235 1237 1242 CONECT 1237 1236 CONECT 1238 1235 1239 CONECT 1239 1238 1240 CONECT 1240 1239 1241 CONECT 1241 1240 CONECT 1242 1236 CONECT 1486 1496 CONECT 1487 1496 CONECT 1496 1486 1487 1497 CONECT 1497 1496 1498 1500 CONECT 1498 1497 1499 1504 CONECT 1499 1498 CONECT 1500 1497 1501 CONECT 1501 1500 1502 CONECT 1502 1501 1503 CONECT 1503 1502 CONECT 1504 1498 CONECT 1675 1986 CONECT 1963 1986 CONECT 1986 1675 1963 2014 CONECT 1988 1989 CONECT 1989 1988 1990 1993 CONECT 1990 1989 1991 CONECT 1991 1990 1992 CONECT 1992 1991 1996 CONECT 1993 1989 1994 1995 CONECT 1994 1993 CONECT 1995 1993 CONECT 1996 1992 1997 CONECT 1997 1996 1998 1999 CONECT 1998 1997 2003 CONECT 1999 1997 2000 2001 CONECT 2000 1999 CONECT 2001 1999 2002 2003 CONECT 2002 2001 CONECT 2003 1998 2001 2004 CONECT 2004 2003 2005 2013 CONECT 2005 2004 2006 CONECT 2006 2005 2007 CONECT 2007 2006 2008 2013 CONECT 2008 2007 2009 2010 CONECT 2009 2008 CONECT 2010 2008 2011 CONECT 2011 2010 2012 CONECT 2012 2011 2013 CONECT 2013 2004 2007 2012 CONECT 2014 1986 2015 2018 CONECT 2015 2014 2016 CONECT 2016 2015 2017 CONECT 2017 2016 2018 CONECT 2018 2014 2017 CONECT 2019 2020 2021 2022 2023 CONECT 2020 2019 CONECT 2021 2019 CONECT 2022 2019 CONECT 2023 2019 CONECT 2024 2025 2026 2027 2028 CONECT 2025 2024 CONECT 2026 2024 CONECT 2027 2024 CONECT 2028 2024 CONECT 2029 2030 2031 2032 2033 CONECT 2030 2029 CONECT 2031 2029 CONECT 2032 2029 CONECT 2033 2029 CONECT 2034 2035 2036 2037 2038 CONECT 2035 2034 CONECT 2036 2034 CONECT 2037 2034 CONECT 2038 2034 CONECT 2039 2040 2041 CONECT 2040 2039 CONECT 2041 2039 2042 CONECT 2042 2041 CONECT 2043 2044 2045 CONECT 2044 2043 CONECT 2045 2043 2046 CONECT 2046 2045 CONECT 2047 2048 2049 CONECT 2048 2047 CONECT 2049 2047 2050 CONECT 2050 2049 CONECT 2051 2052 2053 CONECT 2052 2051 CONECT 2053 2051 2054 CONECT 2054 2053 CONECT 2055 2056 2057 CONECT 2056 2055 CONECT 2057 2055 2058 CONECT 2058 2057 CONECT 2059 2060 2061 CONECT 2060 2059 CONECT 2061 2059 2062 CONECT 2062 2061 CONECT 2063 2064 2065 CONECT 2064 2063 CONECT 2065 2063 2066 CONECT 2066 2065 CONECT 2067 2068 2069 CONECT 2068 2067 CONECT 2069 2067 2070 CONECT 2070 2069 CONECT 2071 2072 2073 CONECT 2072 2071 CONECT 2073 2071 2074 CONECT 2074 2073 MASTER 452 0 21 11 7 0 34 6 2202 1 121 19 END