HEADER TRANSFERASE 25-NOV-08 3FDB TITLE CRYSTAL STRUCTURE OF A PUTATIVE PLP-DEPENDENT BETA-CYSTATHIONASE TITLE 2 (AECD, DIP1736) FROM CORYNEBACTERIUM DIPHTHERIAE AT 1.99 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PLP-DEPENDENT BETA-CYSTATHIONASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA C-S LYASE; COMPND 5 EC: 3.-.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717; SOURCE 4 GENE: AECD, DIP1736, NP_940074.1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PLP-DEPENDENT TRANSFERASE-LIKE FOLD, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 01-FEB-23 3FDB 1 REMARK SEQADV REVDAT 5 24-JUL-19 3FDB 1 REMARK LINK REVDAT 4 01-NOV-17 3FDB 1 REMARK REVDAT 3 13-JUL-11 3FDB 1 VERSN REVDAT 2 23-MAR-11 3FDB 1 HEADER TITLE KEYWDS REVDAT 1 09-DEC-08 3FDB 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE PLP-DEPENDENT JRNL TITL 2 BETA-CYSTATHIONASE (NP_940074.1) FROM CORYNEBACTERIUM JRNL TITL 3 DIPHTHERIAE AT 1.99 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.99 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 41858 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 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 : 2140 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) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2899 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2950 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 431 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 30.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.28000 REMARK 3 B22 (A**2) : 2.28000 REMARK 3 B33 (A**2) : -3.42000 REMARK 3 B12 (A**2) : 1.14000 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): 0.110 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.231 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3138 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2087 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4277 ; 1.471 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5069 ; 0.967 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ; 4.650 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;32.315 ;23.931 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 464 ;11.185 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;12.891 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 458 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3565 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 658 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 672 ; 0.213 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2188 ; 0.196 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1581 ; 0.184 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1435 ; 0.091 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 526 ; 0.182 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.198 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 24 ; 0.233 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 74 ; 0.272 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.248 ; 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): 1931 ; 1.579 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 771 ; 0.480 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3120 ; 2.525 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1260 ; 5.015 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1157 ; 7.027 ;11.000 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 0 A 376 REMARK 3 ORIGIN FOR THE GROUP (A): -12.2433 33.2793 18.8240 REMARK 3 T TENSOR REMARK 3 T11: -0.0893 T22: -0.0802 REMARK 3 T33: -0.0647 T12: -0.0499 REMARK 3 T13: 0.0319 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.4085 L22: 0.6188 REMARK 3 L33: 1.1808 L12: 0.1468 REMARK 3 L13: -0.0760 L23: 0.0426 REMARK 3 S TENSOR REMARK 3 S11: -0.0128 S12: 0.0069 S13: -0.0026 REMARK 3 S21: -0.0614 S22: 0.0366 S23: -0.0029 REMARK 3 S31: -0.0633 S32: 0.1023 S33: -0.0239 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. REMARK 3 4.SODIUM ION, ETHYLENE GLYCOL MOLECULES AND CHLORIDE IONS FROM REMARK 3 CRYSTALLIZATION AND CRYOPROTECTANT ARE MODELED INTO REMARK 3 THISSTRUCTURE, RESPECTIVELY. 5.ONE PLP MOLECULE FROM PROTEIN REMARK 3 EXPRESSION ARE MODELED IN THIS STRUCTURE WITH CLEAR ELECTRON REMARK 3 DENSITY SUPPORT. REMARK 4 REMARK 4 3FDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837,0.97934,0.97922 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47285 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 29.961 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M MGCL2, 10.0000% PEG-3000, 0.1M REMARK 280 CACODYLATE PH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.82000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 143.64000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 143.64000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 71.82000 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 71.82000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL A 378 LIES ON A SPECIAL POSITION. 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 GLN A 22 CG CD OE1 NE2 REMARK 470 GLN A 199 CD OE1 NE2 REMARK 470 GLN A 277 CD OE1 NE2 REMARK 470 GLU A 330 CD OE1 OE2 REMARK 470 LYS A 331 NZ REMARK 470 LYS A 333 CE NZ 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 MSE A 1 SE MSE A 1 CE -0.432 REMARK 500 MSE A 368 SE MSE A 368 CE -0.443 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 TRP A 28 -97.88 -114.64 REMARK 500 LYS A 230 73.05 55.13 REMARK 500 THR A 308 171.09 75.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 377 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 378 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 379 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 382 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 385 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 386 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 387 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 388 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 389 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 390 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 391 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 390709 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 3FDB A 1 376 UNP Q6NFZ9 Q6NFZ9_CORDI 1 376 SEQADV 3FDB GLY A 0 UNP Q6NFZ9 EXPRESSION TAG SEQRES 1 A 377 GLY MSE GLN PHE PRO SER ILE GLU ASP LEU ARG ALA ARG SEQRES 2 A 377 ASN THR MSE LYS TRP THR ARG TYR GLY GLN GLY VAL LEU SEQRES 3 A 377 PRO LEU TRP VAL ALA GLU SER ASP PHE SER THR CYS PRO SEQRES 4 A 377 ALA VAL LEU GLN ALA ILE THR ASP ALA VAL GLN ARG GLU SEQRES 5 A 377 ALA PHE GLY TYR GLN PRO ASP GLY SER LEU LEU SER GLN SEQRES 6 A 377 ALA THR ALA GLU PHE TYR ALA ASP ARG TYR GLY TYR GLN SEQRES 7 A 377 ALA ARG PRO GLU TRP ILE PHE PRO ILE PRO ASP VAL VAL SEQRES 8 A 377 ARG GLY LEU TYR ILE ALA ILE ASP HIS PHE THR PRO ALA SEQRES 9 A 377 GLN SER LYS VAL ILE VAL PRO THR PRO ALA TYR PRO PRO SEQRES 10 A 377 PHE PHE HIS LEU LEU SER ALA THR GLN ARG GLU GLY ILE SEQRES 11 A 377 PHE ILE ASP ALA THR GLY GLY ILE ASN LEU HIS ASP VAL SEQRES 12 A 377 GLU LYS GLY PHE GLN ALA GLY ALA ARG SER ILE LEU LEU SEQRES 13 A 377 CYS ASN PRO TYR ASN PRO LEU GLY MSE VAL PHE ALA PRO SEQRES 14 A 377 GLU TRP LEU ASN GLU LEU CYS ASP LEU ALA HIS ARG TYR SEQRES 15 A 377 ASP ALA ARG VAL LEU VAL ASP GLU ILE HIS ALA PRO LEU SEQRES 16 A 377 VAL PHE ASP GLY GLN HIS THR VAL ALA ALA GLY VAL SER SEQRES 17 A 377 ASP THR ALA ALA SER VAL CYS ILE THR ILE THR ALA PRO SEQRES 18 A 377 SER LLP ALA TRP ASN ILE ALA GLY LEU LYS CYS ALA GLN SEQRES 19 A 377 ILE ILE PHE SER ASN PRO SER ASP ALA GLU HIS TRP GLN SEQRES 20 A 377 GLN LEU SER PRO VAL ILE LYS ASP GLY ALA SER THR LEU SEQRES 21 A 377 GLY LEU ILE ALA ALA GLU ALA ALA TYR ARG TYR GLY THR SEQRES 22 A 377 ASP PHE LEU ASN GLN GLU VAL ALA TYR LEU LYS ASN ASN SEQRES 23 A 377 HIS ASP PHE LEU LEU HIS GLU ILE PRO LYS ARG ILE PRO SEQRES 24 A 377 GLY ALA LYS ILE THR PRO MSE GLN ALA THR TYR LEU MSE SEQRES 25 A 377 TRP ILE ASP PHE ARG ASP THR THR ILE GLU GLY SER PRO SEQRES 26 A 377 SER GLU PHE PHE ILE GLU LYS ALA LYS VAL ALA MSE ASN SEQRES 27 A 377 ASP GLY ALA TRP PHE GLY GLU ASP GLY THR GLY PHE CYS SEQRES 28 A 377 ARG LEU ASN PHE ALA THR SER ARG GLU VAL LEU GLU GLU SEQRES 29 A 377 ALA ILE ASP ARG MSE ALA LYS ALA VAL SER HIS HIS THR MODRES 3FDB MSE A 1 MET SELENOMETHIONINE MODRES 3FDB MSE A 15 MET SELENOMETHIONINE MODRES 3FDB MSE A 164 MET SELENOMETHIONINE MODRES 3FDB LLP A 222 LYS MODRES 3FDB MSE A 305 MET SELENOMETHIONINE MODRES 3FDB MSE A 311 MET SELENOMETHIONINE MODRES 3FDB MSE A 336 MET SELENOMETHIONINE MODRES 3FDB MSE A 368 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 15 8 HET MSE A 164 8 HET LLP A 222 24 HET MSE A 305 8 HET MSE A 311 8 HET MSE A 336 8 HET MSE A 368 8 HET NA A 377 1 HET CL A 378 1 HET CL A 379 1 HET CL A 380 1 HET CL A 381 1 HET CL A 382 1 HET EDO A 383 4 HET EDO A 384 4 HET EDO A 385 4 HET EDO A 386 4 HET EDO A 387 4 HET EDO A 388 4 HET EDO A 389 4 HET EDO A 390 4 HET EDO A 391 4 HETNAM MSE SELENOMETHIONINE HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 NA NA 1+ FORMUL 3 CL 5(CL 1-) FORMUL 8 EDO 9(C2 H6 O2) FORMUL 17 HOH *431(H2 O) HELIX 1 1 SER A 5 ARG A 12 1 8 HELIX 2 2 THR A 14 ARG A 19 1 6 HELIX 3 3 CYS A 37 ARG A 50 1 14 HELIX 4 4 LEU A 61 GLY A 75 1 15 HELIX 5 5 ARG A 79 GLU A 81 5 3 HELIX 6 6 ASP A 88 THR A 101 1 14 HELIX 7 7 PRO A 115 GLN A 125 1 11 HELIX 8 8 ASN A 138 ALA A 148 1 11 HELIX 9 9 ALA A 167 TYR A 181 1 15 HELIX 10 10 HIS A 191 VAL A 195 5 5 HELIX 11 11 VAL A 202 VAL A 206 5 5 HELIX 12 12 SER A 207 VAL A 213 1 7 HELIX 13 13 ILE A 226 LYS A 230 5 5 HELIX 14 14 ASN A 238 LEU A 248 1 11 HELIX 15 15 SER A 249 ASP A 254 1 6 HELIX 16 16 SER A 257 GLY A 271 1 15 HELIX 17 17 GLY A 271 ILE A 297 1 27 HELIX 18 18 SER A 323 LYS A 333 1 11 HELIX 19 19 ALA A 340 THR A 347 5 8 HELIX 20 20 SER A 357 SER A 373 1 17 SHEET 1 A 2 LEU A 25 PRO A 26 0 SHEET 2 A 2 VAL A 334 ALA A 335 1 O ALA A 335 N LEU A 25 SHEET 1 B 7 ILE A 83 ILE A 86 0 SHEET 2 B 7 ALA A 232 ILE A 235 -1 O ALA A 232 N ILE A 86 SHEET 3 B 7 CYS A 214 THR A 218 -1 N THR A 216 O ILE A 235 SHEET 4 B 7 ARG A 184 ASP A 188 1 N VAL A 187 O ILE A 217 SHEET 5 B 7 SER A 152 CYS A 156 1 N LEU A 155 O LEU A 186 SHEET 6 B 7 VAL A 107 THR A 111 1 N ILE A 108 O LEU A 154 SHEET 7 B 7 GLY A 128 ASP A 132 1 O ILE A 131 N THR A 111 SHEET 1 C 4 LYS A 301 ILE A 302 0 SHEET 2 C 4 LEU A 310 ASP A 314 -1 O ASP A 314 N LYS A 301 SHEET 3 C 4 PHE A 349 ASN A 353 -1 O CYS A 350 N ILE A 313 SHEET 4 C 4 ASN A 337 ASP A 338 -1 N ASN A 337 O ARG A 351 LINK C GLY A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N GLN A 2 1555 1555 1.33 LINK C THR A 14 N MSE A 15 1555 1555 1.32 LINK C MSE A 15 N LYS A 16 1555 1555 1.33 LINK C GLY A 163 N MSE A 164 1555 1555 1.33 LINK C MSE A 164 N VAL A 165 1555 1555 1.34 LINK C SER A 221 N LLP A 222 1555 1555 1.34 LINK C LLP A 222 N ALA A 223 1555 1555 1.32 LINK C PRO A 304 N MSE A 305 1555 1555 1.32 LINK C MSE A 305 N AGLN A 306 1555 1555 1.33 LINK C MSE A 305 N BGLN A 306 1555 1555 1.33 LINK C LEU A 310 N MSE A 311 1555 1555 1.33 LINK C MSE A 311 N TRP A 312 1555 1555 1.33 LINK C ALA A 335 N MSE A 336 1555 1555 1.34 LINK C MSE A 336 N ASN A 337 1555 1555 1.34 LINK C ARG A 367 N MSE A 368 1555 1555 1.33 LINK C MSE A 368 N ALA A 369 1555 1555 1.34 LINK OP2 LLP A 222 NA NA A 377 1555 1555 2.21 CISPEP 1 THR A 111 PRO A 112 0 2.17 CISPEP 2 ASN A 157 PRO A 158 0 0.76 CISPEP 3 ASN A 160 PRO A 161 0 5.64 SITE 1 AC1 6 ASP A 88 VAL A 89 ALA A 219 SER A 221 SITE 2 AC1 6 LLP A 222 HOH A 640 SITE 1 AC2 2 PRO A 87 GLY A 255 SITE 1 AC3 4 ALA A 30 ARG A 351 HOH A 583 HOH A 596 SITE 1 AC4 3 CYS A 37 PRO A 38 ALA A 39 SITE 1 AC5 6 ASP A 88 ARG A 91 ASP A 254 GLY A 255 SITE 2 AC5 6 HOH A 603 HOH A 663 SITE 1 AC6 4 ASN A 160 PRO A 161 PHE A 342 ARG A 351 SITE 1 AC7 5 PRO A 4 SER A 5 ILE A 6 SER A 357 SITE 2 AC7 5 GLU A 359 SITE 1 AC8 7 PHE A 196 VAL A 279 ALA A 280 HOH A 433 SITE 2 AC8 7 HOH A 608 HOH A 621 HOH A 810 SITE 1 AC9 3 GLY A 343 EDO A 391 HOH A 600 SITE 1 BC1 5 GLU A 173 ARG A 180 PRO A 294 HOH A 731 SITE 2 BC1 5 HOH A 753 SITE 1 BC2 6 TYR A 94 ILE A 95 ASP A 98 HIS A 99 SITE 2 BC2 6 HOH A 633 HOH A 802 SITE 1 BC3 5 PHE A 315 ARG A 316 THR A 318 ILE A 320 SITE 2 BC3 5 GLY A 322 SITE 1 BC4 1 MSE A 15 SITE 1 BC5 2 TRP A 341 HOH A 659 SITE 1 BC6 5 GLY A 343 GLU A 344 EDO A 385 HOH A 610 SITE 2 BC6 5 HOH A 711 CRYST1 69.180 69.180 215.460 90.00 90.00 120.00 P 31 2 1 6 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 0.014455 0.008346 0.000000 0.00000 SCALE2 0.000000 0.016691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004641 0.00000