HEADER LYASE 06-JUN-18 6DNJ TITLE DIRECTED EVOLUTIONARY CHANGES IN KEMP ELIMINASE KE07 - CRYSTAL 28 TITLE 2 ROUND 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: KEMP ELIMINASE KE07; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DIRECTED EVOLUTION, DE NOVO PROTEIN, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR C.J.JACKSON,N.-S.HONG,P.D.CARR REVDAT 3 11-OCT-23 6DNJ 1 REMARK REVDAT 2 13-FEB-19 6DNJ 1 JRNL REVDAT 1 01-AUG-18 6DNJ 0 JRNL AUTH N.S.HONG,D.PETROVIC,R.LEE,G.GRYN'OVA,M.PURG,J.SAUNDERS, JRNL AUTH 2 P.BAUER,P.D.CARR,C.Y.LIN,P.D.MABBITT,W.ZHANG,T.ALTAMORE, JRNL AUTH 3 C.EASTON,M.L.COOTE,S.C.L.KAMERLIN,C.J.JACKSON JRNL TITL THE EVOLUTION OF MULTIPLE ACTIVE SITE CONFIGURATIONS IN A JRNL TITL 2 DESIGNED ENZYME. JRNL REF NAT COMMUN V. 9 3900 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30254369 JRNL DOI 10.1038/S41467-018-06305-Y REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 50485 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2666 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3640 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 193 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1952 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 274 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : 0.39000 REMARK 3 B33 (A**2) : -1.25000 REMARK 3 B12 (A**2) : 0.19000 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.766 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2061 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2023 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2787 ; 1.297 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4650 ; 1.022 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 261 ; 5.898 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;36.783 ;23.871 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 374 ;13.324 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;15.907 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 315 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2337 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 463 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1029 ; 1.931 ; 2.359 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1028 ; 1.830 ; 2.352 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1295 ; 2.817 ; 3.525 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1296 ; 2.980 ; 3.533 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1032 ; 2.867 ; 2.891 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1033 ; 2.866 ; 2.890 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1493 ; 3.753 ; 4.126 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2404 ; 4.164 ;30.149 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2405 ; 4.163 ;30.142 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4084 ; 2.663 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 114 ;11.039 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4207 ;12.708 ; 5.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6DNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 1.11.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52414 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 42.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.80 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 2.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5C7M REMARK 200 REMARK 200 REMARK: NULL 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: 25 MM HEPES, PH 7.25, 0.1 M NACL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 52.05700 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 104.11400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 78.08550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 130.14250 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 26.02850 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.05700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 104.11400 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 130.14250 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 78.08550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.02850 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: 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 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 HOH A 546 LIES ON A SPECIAL POSITION. 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 MET A 0 REMARK 465 ALA A 1 REMARK 465 GLY A 252 REMARK 465 LEU A 253 REMARK 465 GLY A 254 REMARK 465 SER A 255 REMARK 465 LEU A 256 REMARK 465 GLU A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 HIS A 262 REMARK 465 HIS A 263 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 639 O HOH A 639 8555 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 154 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 154 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 SER A 55 -143.29 -11.65 REMARK 500 VAL A 56 -82.10 64.42 REMARK 500 ASN A 103 -82.36 -136.48 REMARK 500 ARG A 202 130.18 85.47 REMARK 500 ARG A 202 127.82 83.06 REMARK 500 ASP A 224 -83.72 -141.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 54 SER A 55 -138.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 673 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A 674 DISTANCE = 16.06 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MPD A 301 and H5J A REMARK 800 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MPD A 301 and H5J A REMARK 800 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MPD A 301 and H5J A REMARK 800 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MPD A 301 and H5J A REMARK 800 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MPD A 301 and H5J A REMARK 800 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MPD A 301 and H5J A REMARK 800 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MPD A 301 and H5J A REMARK 800 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MPD A 301 and H5J A REMARK 800 302 DBREF 6DNJ A 0 263 PDB 6DNJ 6DNJ 0 263 SEQRES 1 A 264 MET ALA LEU ALA LYS ARG ILE ASP ALA ALA LEU ILE MET SEQRES 2 A 264 LYS ASP GLY ARG VAL VAL LYS GLY SER ASN PHE GLU ASN SEQRES 3 A 264 LEU ARG ASP SER GLY ASP PRO VAL GLU LEU GLY LYS PHE SEQRES 4 A 264 TYR SER GLU ILE GLY ILE ASP GLU LEU SER PHE TRP ASP SEQRES 5 A 264 ILE THR ALA SER VAL GLU LYS ARG LYS THR MET LEU GLU SEQRES 6 A 264 LEU VAL GLU LYS VAL ALA GLU GLN ILE ASP ILE PRO PHE SEQRES 7 A 264 THR VAL GLY GLY GLY ILE HIS ASP PHE GLU THR ALA SER SEQRES 8 A 264 GLU LEU ILE LEU ARG GLY ALA ASP LYS VAL GLU ILE ASN SEQRES 9 A 264 THR ALA ALA VAL GLU ASN PRO SER LEU ILE THR GLN ILE SEQRES 10 A 264 ALA GLN THR PHE GLY SER GLN ALA VAL VAL VAL TYR ILE SEQRES 11 A 264 ALA ALA LYS ARG VAL ASP GLY GLU PHE MET VAL PHE THR SEQRES 12 A 264 TYR SER GLY LYS LYS ASN THR GLY ILE LEU LEU ARG ASP SEQRES 13 A 264 TRP VAL VAL GLU VAL GLU LYS ARG GLY ALA GLY GLU ILE SEQRES 14 A 264 VAL LEU GLY SER ILE ASP ARG LEU GLY THR LYS SER GLY SEQRES 15 A 264 TYR ASP THR GLU MET ILE ARG PHE VAL ARG PRO LEU THR SEQRES 16 A 264 THR LEU PRO ILE ILE ALA HIS ARG GLY ALA GLY LYS MET SEQRES 17 A 264 GLU HIS PHE LEU GLU ALA PHE LEU ALA GLY ALA ASP ALA SEQRES 18 A 264 ALA LYS ALA ASP SER VAL PHE HIS PHE ARG GLU ILE ASP SEQRES 19 A 264 VAL ARG GLU LEU LYS GLU TYR LEU LYS LYS HIS GLY VAL SEQRES 20 A 264 ASN VAL ARG LEU GLU GLY LEU GLY SER LEU GLU HIS HIS SEQRES 21 A 264 HIS HIS HIS HIS HET MPD A 301 8 HET H5J A 302 12 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM H5J 5-NITRO-1,2-BENZOXAZOLE FORMUL 2 MPD C6 H14 O2 FORMUL 3 H5J C7 H4 N2 O3 FORMUL 4 HOH *274(H2 O) HELIX 1 AA1 ASP A 31 GLY A 43 1 13 HELIX 2 AA2 GLU A 57 ILE A 73 1 17 HELIX 3 AA3 ASP A 85 GLY A 96 1 12 HELIX 4 AA4 ASN A 103 ASN A 109 1 7 HELIX 5 AA5 PRO A 110 GLY A 121 1 12 HELIX 6 AA6 LEU A 153 GLY A 164 1 12 HELIX 7 AA7 ASP A 174 LEU A 176 5 3 HELIX 8 AA8 ASP A 183 ARG A 191 1 9 HELIX 9 AA9 PRO A 192 THR A 194 5 3 HELIX 10 AB1 LYS A 206 ALA A 216 1 11 HELIX 11 AB2 ASP A 224 PHE A 229 1 6 HELIX 12 AB3 ASP A 233 HIS A 244 1 12 SHEET 1 AA1 8 ARG A 16 VAL A 17 0 SHEET 2 AA1 8 ARG A 5 LYS A 13 -1 N LYS A 13 O ARG A 16 SHEET 3 AA1 8 GLU A 46 ASP A 51 1 O TRP A 50 N MET A 12 SHEET 4 AA1 8 PHE A 77 GLY A 80 1 O THR A 78 N PHE A 49 SHEET 5 AA1 8 LYS A 99 ILE A 102 1 O GLU A 101 N VAL A 79 SHEET 6 AA1 8 VAL A 125 VAL A 134 1 O VAL A 126 N VAL A 100 SHEET 7 AA1 8 GLU A 137 THR A 142 -1 O PHE A 141 N ALA A 130 SHEET 8 AA1 8 LYS A 147 LEU A 152 -1 O ILE A 151 N VAL A 140 SHEET 1 AA2 8 ARG A 16 VAL A 17 0 SHEET 2 AA2 8 ARG A 5 LYS A 13 -1 N LYS A 13 O ARG A 16 SHEET 3 AA2 8 ALA A 220 ALA A 223 1 O ALA A 223 N ALA A 9 SHEET 4 AA2 8 ILE A 198 HIS A 201 1 N ALA A 200 O LYS A 222 SHEET 5 AA2 8 GLU A 167 SER A 172 1 N ILE A 168 O ILE A 199 SHEET 6 AA2 8 VAL A 125 VAL A 134 1 N ILE A 129 O VAL A 169 SHEET 7 AA2 8 GLU A 137 THR A 142 -1 O PHE A 141 N ALA A 130 SHEET 8 AA2 8 LYS A 147 LEU A 152 -1 O ILE A 151 N VAL A 140 LINK C1 MPD A 301 CAE H5J A 302 1555 1555 1.62 LINK C2 MPD A 301 CAF H5J A 302 1555 1555 1.08 LINK C2 MPD A 301 CAJ H5J A 302 1555 1555 1.59 LINK CM MPD A 301 CAI H5J A 302 1555 1555 1.57 LINK CM MPD A 301 CAF H5J A 302 1555 1555 1.17 LINK CM MPD A 301 CAJ H5J A 302 1555 1555 1.61 LINK C3 MPD A 301 CAF H5J A 302 1555 1555 1.51 LINK O4 MPD A 301 CAK H5J A 302 1555 1555 1.54 SITE 1 AC1 11 TRP A 50 ILE A 52 GLY A 80 GLY A 81 SITE 2 AC1 11 GLU A 101 ASN A 103 TYR A 128 HOH A 402 SITE 3 AC1 11 HOH A 404 HOH A 430 HOH A 674 SITE 1 AC2 11 TRP A 50 ILE A 52 GLY A 80 GLY A 81 SITE 2 AC2 11 GLU A 101 ASN A 103 TYR A 128 HOH A 402 SITE 3 AC2 11 HOH A 404 HOH A 430 HOH A 674 SITE 1 AC3 11 TRP A 50 ILE A 52 GLY A 80 GLY A 81 SITE 2 AC3 11 GLU A 101 ASN A 103 TYR A 128 HOH A 402 SITE 3 AC3 11 HOH A 404 HOH A 430 HOH A 674 SITE 1 AC4 11 TRP A 50 ILE A 52 GLY A 80 GLY A 81 SITE 2 AC4 11 GLU A 101 ASN A 103 TYR A 128 HOH A 402 SITE 3 AC4 11 HOH A 404 HOH A 430 HOH A 674 SITE 1 AC5 11 TRP A 50 ILE A 52 GLY A 80 GLY A 81 SITE 2 AC5 11 GLU A 101 ASN A 103 TYR A 128 HOH A 402 SITE 3 AC5 11 HOH A 404 HOH A 430 HOH A 674 SITE 1 AC6 11 TRP A 50 ILE A 52 GLY A 80 GLY A 81 SITE 2 AC6 11 GLU A 101 ASN A 103 TYR A 128 HOH A 402 SITE 3 AC6 11 HOH A 404 HOH A 430 HOH A 674 SITE 1 AC7 11 TRP A 50 ILE A 52 GLY A 80 GLY A 81 SITE 2 AC7 11 GLU A 101 ASN A 103 TYR A 128 HOH A 402 SITE 3 AC7 11 HOH A 404 HOH A 430 HOH A 674 SITE 1 AC8 11 TRP A 50 ILE A 52 GLY A 80 GLY A 81 SITE 2 AC8 11 GLU A 101 ASN A 103 TYR A 128 HOH A 402 SITE 3 AC8 11 HOH A 404 HOH A 430 HOH A 674 CRYST1 97.350 97.350 156.171 90.00 90.00 120.00 P 61 2 2 12 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 0.010272 0.005931 0.000000 0.00000 SCALE2 0.000000 0.011861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006403 0.00000