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 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