PDB Short entry for 7D49 HEADER OXIDOREDUCTASE 23-SEP-20 7D49 TITLE X-RAY CRYSTAL STRUCTURE OF E.COLI DIHYDROFOLATE REDUCTASE COMPLEXED TITLE 2 WITH FOLATE AND NADP+ AT PH4.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: FOLA, TMRA, B0048, JW0047; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-SUMO KEYWDS DIHYDROFOLATE, REDUCTASE, ALPHA-BETA SANDIWITCH, NADPH, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION NUMMDL 80 AUTHOR Q.WAN,C.DEALWIS REVDAT 2 29-NOV-23 7D49 1 REMARK REVDAT 1 09-JUN-21 7D49 0 JRNL AUTH Q.WAN,B.C.BENNETT,T.WYMORE,Z.LI,M.A.WILSON,C.L.BROOKS III, JRNL AUTH 2 P.LANGAN,A.KOVALEVSKY,C.G.DEALWIS JRNL TITL CAPTURING THE CATALYTIC PROTON OF DIHYDROFOLATE REDUCTASE: JRNL TITL 2 IMPLICATIONS FOR GENERAL ACID-BASE CATALYSIS JRNL REF ACS CATALYSIS V. 11 5873 2021 JRNL REFN ESSN 2155-5435 JRNL DOI 10.1021/ACSCATAL.1C00417 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.ENSEMBLE_REFINEMENT:1.13RC2_2986) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 17682 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.9991 - 2.3809 0.97 2962 165 0.1384 0.1859 REMARK 3 2 2.3809 - 2.0801 0.97 2954 141 0.1311 0.1782 REMARK 3 3 2.0801 - 1.8899 0.97 2877 183 0.1331 0.1895 REMARK 3 4 1.8899 - 1.7545 0.94 2809 158 0.1414 0.1936 REMARK 3 5 1.7545 - 1.6511 0.71 2114 116 0.1859 0.2188 REMARK 3 6 1.7500 - 1.6510 0.95 3062 141 0.1268 0.1326 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7D49 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018694. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5 REMARK 200 MONOCHROMATOR : CHOPPER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18163 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.3000 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) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1RX2 REMARK 200 REMARK 200 REMARK: LONG RECTANGULAR CRYSTAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40MG/ML DHFR-FOLATE-NADP+ COMPLEX, 12% REMARK 280 (V/V) PEG 400, 100MM MNCL2, 100MM NAAC, PH4.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 17.05100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.55650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.79750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.55650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.05100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.79750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 2170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 11 CYS A 152 CB CYS A 152 SG -0.121 REMARK 500 18 MET A 1 CG MET A 1 SD -0.157 REMARK 500 25 CYS A 152 CB CYS A 152 SG 0.135 REMARK 500 38 ARG A 98 CG ARG A 98 CD -0.167 REMARK 500 68 ARG A 12 CG ARG A 12 CD -0.175 REMARK 500 68 GLU A 134 CG GLU A 134 CD 0.094 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 1 CYS A 152 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 3 MET A 16 CA - CB - CG ANGL. DEV. = -11.4 DEGREES REMARK 500 3 MET A 16 CG - SD - CE ANGL. DEV. = 13.0 DEGREES REMARK 500 7 CYS A 152 CA - CB - SG ANGL. DEV. = 10.6 DEGREES REMARK 500 8 CYS A 152 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 9 CYS A 152 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 13 CYS A 152 CA - CB - SG ANGL. DEV. = 10.6 DEGREES REMARK 500 18 MET A 1 CB - CG - SD ANGL. DEV. = 18.8 DEGREES REMARK 500 23 CYS A 152 CA - CB - SG ANGL. DEV. = 9.6 DEGREES REMARK 500 24 CYS A 152 CA - CB - SG ANGL. DEV. = 8.8 DEGREES REMARK 500 25 CYS A 152 CA - CB - SG ANGL. DEV. = 8.9 DEGREES REMARK 500 33 GLY A 86 C - N - CA ANGL. DEV. = 13.0 DEGREES REMARK 500 37 LEU A 24 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 37 PRO A 25 C - N - CD ANGL. DEV. = -20.6 DEGREES REMARK 500 38 LEU A 24 CA - CB - CG ANGL. DEV. = 19.7 DEGREES REMARK 500 39 CYS A 152 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 40 LEU A 24 CA - CB - CG ANGL. DEV. = 15.9 DEGREES REMARK 500 53 CYS A 152 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 58 CYS A 152 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 63 ARG A 98 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 64 CYS A 152 CA - CB - SG ANGL. DEV. = 10.5 DEGREES REMARK 500 68 MET A 1 CG - SD - CE ANGL. DEV. = 15.9 DEGREES REMARK 500 68 ARG A 12 CB - CG - CD ANGL. DEV. = 19.1 DEGREES REMARK 500 71 LEU A 28 CA - CB - CG ANGL. DEV. = -17.1 DEGREES REMARK 500 73 CYS A 152 CA - CB - SG ANGL. DEV. = 10.1 DEGREES REMARK 500 74 CYS A 152 CA - CB - SG ANGL. DEV. = 8.4 DEGREES REMARK 500 75 LEU A 62 CA - CB - CG ANGL. DEV. = 13.9 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 1 ASP A 69 112.73 -161.58 REMARK 500 1 ASP A 87 65.88 -108.23 REMARK 500 1 TYR A 128 -156.61 -84.66 REMARK 500 1 ASP A 144 -156.64 -133.06 REMARK 500 2 LEU A 24 85.94 -150.14 REMARK 500 2 ASP A 69 113.71 -170.94 REMARK 500 2 GLU A 139 127.56 -171.79 REMARK 500 2 CYS A 152 111.41 -160.76 REMARK 500 3 PRO A 21 76.58 -102.08 REMARK 500 3 ASP A 69 111.70 -175.69 REMARK 500 3 GLU A 90 123.79 -171.11 REMARK 500 3 PHE A 137 126.67 -179.98 REMARK 500 3 SER A 148 33.03 -92.57 REMARK 500 4 GLU A 17 60.62 29.16 REMARK 500 5 ASP A 69 113.92 -171.10 REMARK 500 6 ASN A 18 50.19 80.25 REMARK 500 6 TRP A 22 -174.91 -178.34 REMARK 500 6 ASP A 69 124.52 -170.01 REMARK 500 7 PRO A 21 48.95 -91.69 REMARK 500 7 ASP A 69 109.65 -165.37 REMARK 500 7 PRO A 126 -148.47 -67.55 REMARK 500 7 PRO A 130 -64.34 -27.53 REMARK 500 7 PHE A 137 142.16 -177.69 REMARK 500 8 PRO A 53 170.27 -52.19 REMARK 500 8 ASP A 69 115.76 -170.77 REMARK 500 8 ALA A 84 3.34 -69.92 REMARK 500 8 PRO A 126 -141.62 -62.88 REMARK 500 8 GLU A 139 112.52 -170.99 REMARK 500 9 GLU A 17 80.18 50.14 REMARK 500 9 ASN A 18 55.27 5.26 REMARK 500 9 ASP A 127 57.19 -63.55 REMARK 500 9 TYR A 128 74.25 -49.07 REMARK 500 9 CYS A 152 96.33 -160.18 REMARK 500 10 ASP A 69 108.73 -167.59 REMARK 500 11 THR A 68 16.41 -141.83 REMARK 500 11 PHE A 137 119.81 174.44 REMARK 500 12 ASP A 69 117.05 -172.20 REMARK 500 12 GLU A 129 101.46 -55.86 REMARK 500 12 GLU A 139 102.98 -168.01 REMARK 500 13 GLU A 17 51.47 38.50 REMARK 500 13 ASP A 69 110.37 -166.39 REMARK 500 13 ASP A 87 71.65 -117.34 REMARK 500 13 ASP A 122 -6.80 -151.31 REMARK 500 13 PHE A 137 136.22 175.13 REMARK 500 13 GLU A 139 118.93 -170.90 REMARK 500 14 ASN A 18 16.27 81.04 REMARK 500 14 ASP A 69 115.69 -164.63 REMARK 500 14 ASP A 127 147.90 -34.97 REMARK 500 14 GLU A 129 94.64 -36.37 REMARK 500 15 PRO A 21 49.28 -66.02 REMARK 500 REMARK 500 THIS ENTRY HAS 456 RAMACHANDRAN OUTLIERS. 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 TYR A 128 GLU A 129 1 -149.03 REMARK 500 ASP A 127 TYR A 128 8 147.36 REMARK 500 TYR A 128 GLU A 129 8 148.70 REMARK 500 GLU A 129 PRO A 130 10 -140.94 REMARK 500 PRO A 126 ASP A 127 14 142.08 REMARK 500 PRO A 126 ASP A 127 18 131.75 REMARK 500 MET A 20 PRO A 21 20 -149.25 REMARK 500 TRP A 22 ASN A 23 23 149.94 REMARK 500 TYR A 128 GLU A 129 27 -142.53 REMARK 500 VAL A 119 GLU A 120 29 -139.74 REMARK 500 GLN A 65 PRO A 66 35 -146.02 REMARK 500 TRP A 22 ASN A 23 36 -141.68 REMARK 500 GLN A 65 PRO A 66 36 -140.91 REMARK 500 PRO A 66 GLY A 67 36 139.44 REMARK 500 PRO A 66 GLY A 67 37 146.13 REMARK 500 TRP A 22 ASN A 23 38 -147.64 REMARK 500 GLN A 65 PRO A 66 38 -133.64 REMARK 500 GLY A 67 THR A 68 39 -145.29 REMARK 500 ASN A 23 LEU A 24 41 141.11 REMARK 500 GLN A 65 PRO A 66 41 145.24 REMARK 500 ASN A 18 ALA A 19 42 142.63 REMARK 500 ASN A 23 LEU A 24 42 112.24 REMARK 500 PRO A 130 ASP A 131 42 143.02 REMARK 500 GLU A 17 ASN A 18 43 -146.99 REMARK 500 ASN A 18 ALA A 19 43 138.07 REMARK 500 SER A 63 SER A 64 43 143.06 REMARK 500 ASN A 18 ALA A 19 44 131.11 REMARK 500 GLN A 65 PRO A 66 44 148.59 REMARK 500 SER A 64 GLN A 65 45 146.23 REMARK 500 GLN A 65 PRO A 66 45 138.00 REMARK 500 GLN A 65 PRO A 66 46 144.32 REMARK 500 SER A 64 GLN A 65 47 138.59 REMARK 500 PRO A 66 GLY A 67 53 147.90 REMARK 500 PRO A 21 TRP A 22 56 142.90 REMARK 500 GLN A 65 PRO A 66 56 -146.75 REMARK 500 PRO A 66 GLY A 67 56 -117.35 REMARK 500 GLU A 17 ASN A 18 57 -143.04 REMARK 500 PRO A 66 GLY A 67 57 -131.26 REMARK 500 GLY A 86 ASP A 87 58 -143.94 REMARK 500 ASP A 87 VAL A 88 58 -145.84 REMARK 500 PRO A 66 GLY A 67 60 128.92 REMARK 500 ASP A 127 TYR A 128 60 -145.23 REMARK 500 TRP A 22 ASN A 23 65 147.83 REMARK 500 ASP A 127 TYR A 128 65 -142.55 REMARK 500 ASP A 87 VAL A 88 70 -148.21 REMARK 500 ALA A 19 MET A 20 75 144.87 REMARK 500 GLU A 129 PRO A 130 76 -146.34 REMARK 500 MET A 20 PRO A 21 80 -148.05 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 361 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 372 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A 372 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 372 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 373 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A 371 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 371 DISTANCE = 6.28 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 202 DBREF 7D49 A 1 159 UNP P0ABQ4 DYR_ECOLI 1 159 SEQADV 7D49 ASP A 37 UNP P0ABQ4 ASN 37 CONFLICT SEQRES 1 A 159 MET ILE SER LEU ILE ALA ALA LEU ALA VAL ASP ARG VAL SEQRES 2 A 159 ILE GLY MET GLU ASN ALA MET PRO TRP ASN LEU PRO ALA SEQRES 3 A 159 ASP LEU ALA TRP PHE LYS ARG ASN THR LEU ASP LYS PRO SEQRES 4 A 159 VAL ILE MET GLY ARG HIS THR TRP GLU SER ILE GLY ARG SEQRES 5 A 159 PRO LEU PRO GLY ARG LYS ASN ILE ILE LEU SER SER GLN SEQRES 6 A 159 PRO GLY THR ASP ASP ARG VAL THR TRP VAL LYS SER VAL SEQRES 7 A 159 ASP GLU ALA ILE ALA ALA CYS GLY ASP VAL PRO GLU ILE SEQRES 8 A 159 MET VAL ILE GLY GLY GLY ARG VAL TYR GLU GLN PHE LEU SEQRES 9 A 159 PRO LYS ALA GLN LYS LEU TYR LEU THR HIS ILE ASP ALA SEQRES 10 A 159 GLU VAL GLU GLY ASP THR HIS PHE PRO ASP TYR GLU PRO SEQRES 11 A 159 ASP ASP TRP GLU SER VAL PHE SER GLU PHE HIS ASP ALA SEQRES 12 A 159 ASP ALA GLN ASN SER HIS SER TYR CYS PHE GLU ILE LEU SEQRES 13 A 159 GLU ARG ARG HET FOL A 201 32 HET NAP A 202 48 HETNAM FOL FOLIC ACID HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 FOL C19 H19 N7 O6 FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 HOH *79(H2 O) HELIX 1 AA1 ALA A 9 ASP A 11 5 3 HELIX 2 AA2 LEU A 24 LEU A 36 1 13 HELIX 3 AA3 ARG A 44 GLY A 51 1 8 HELIX 4 AA4 SER A 77 CYS A 85 1 9 HELIX 5 AA5 GLY A 96 LEU A 104 1 9 HELIX 6 AA6 PRO A 105 ALA A 107 5 3 SHEET 1 AA1 8 THR A 73 VAL A 75 0 SHEET 2 AA1 8 LYS A 58 LEU A 62 1 N ILE A 61 O THR A 73 SHEET 3 AA1 8 PRO A 39 GLY A 43 1 N VAL A 40 O LYS A 58 SHEET 4 AA1 8 ILE A 91 VAL A 93 1 O MET A 92 N ILE A 41 SHEET 5 AA1 8 ILE A 2 LEU A 8 1 N SER A 3 O ILE A 91 SHEET 6 AA1 8 LYS A 109 ILE A 115 1 O ILE A 115 N LEU A 8 SHEET 7 AA1 8 TYR A 151 ARG A 158 -1 O GLU A 154 N LEU A 112 SHEET 8 AA1 8 TRP A 133 HIS A 141 -1 N GLU A 139 O PHE A 153 SHEET 1 AA2 2 VAL A 13 GLY A 15 0 SHEET 2 AA2 2 THR A 123 HIS A 124 -1 O THR A 123 N ILE A 14 CISPEP 1 GLY A 95 GLY A 96 1 7.04 CISPEP 2 GLY A 95 GLY A 96 2 9.88 CISPEP 3 GLY A 95 GLY A 96 3 10.95 CISPEP 4 GLY A 95 GLY A 96 4 5.15 CISPEP 5 GLY A 95 GLY A 96 5 5.05 CISPEP 6 GLY A 95 GLY A 96 6 1.70 CISPEP 7 GLY A 95 GLY A 96 7 8.14 CISPEP 8 GLY A 95 GLY A 96 8 8.20 CISPEP 9 GLY A 95 GLY A 96 9 8.70 CISPEP 10 GLY A 95 GLY A 96 10 12.51 CISPEP 11 GLY A 95 GLY A 96 11 6.89 CISPEP 12 GLY A 95 GLY A 96 12 7.10 CISPEP 13 GLY A 95 GLY A 96 13 5.93 CISPEP 14 GLY A 95 GLY A 96 14 5.97 CISPEP 15 GLY A 95 GLY A 96 15 4.81 CISPEP 16 GLY A 95 GLY A 96 16 6.21 CISPEP 17 GLY A 95 GLY A 96 17 7.36 CISPEP 18 GLY A 95 GLY A 96 18 10.01 CISPEP 19 GLY A 95 GLY A 96 19 9.34 CISPEP 20 GLY A 95 GLY A 96 20 12.67 CISPEP 21 GLY A 95 GLY A 96 21 7.58 CISPEP 22 GLY A 95 GLY A 96 22 4.32 CISPEP 23 GLY A 95 GLY A 96 23 0.26 CISPEP 24 GLY A 95 GLY A 96 24 2.40 CISPEP 25 GLY A 95 GLY A 96 25 2.92 CISPEP 26 GLY A 95 GLY A 96 26 6.24 CISPEP 27 GLY A 95 GLY A 96 27 9.80 CISPEP 28 GLY A 95 GLY A 96 28 5.01 CISPEP 29 GLY A 95 GLY A 96 29 11.27 CISPEP 30 GLY A 95 GLY A 96 30 15.12 CISPEP 31 GLY A 95 GLY A 96 31 13.40 CISPEP 32 GLY A 95 GLY A 96 32 4.77 CISPEP 33 GLY A 95 GLY A 96 33 5.30 CISPEP 34 GLY A 95 GLY A 96 34 8.04 CISPEP 35 GLY A 95 GLY A 96 35 10.11 CISPEP 36 GLY A 95 GLY A 96 36 8.36 CISPEP 37 GLY A 95 GLY A 96 37 15.78 CISPEP 38 GLY A 95 GLY A 96 38 5.80 CISPEP 39 GLY A 95 GLY A 96 39 6.17 CISPEP 40 GLY A 95 GLY A 96 40 7.70 CISPEP 41 GLY A 95 GLY A 96 41 6.20 CISPEP 42 GLY A 95 GLY A 96 42 7.09 CISPEP 43 GLY A 95 GLY A 96 43 7.33 CISPEP 44 GLY A 95 GLY A 96 44 7.09 CISPEP 45 GLY A 95 GLY A 96 45 5.84 CISPEP 46 GLY A 95 GLY A 96 46 3.99 CISPEP 47 GLY A 95 GLY A 96 47 1.61 CISPEP 48 GLY A 95 GLY A 96 48 7.69 CISPEP 49 GLY A 95 GLY A 96 49 -0.68 CISPEP 50 GLY A 95 GLY A 96 50 2.75 CISPEP 51 GLY A 95 GLY A 96 51 8.19 CISPEP 52 GLY A 95 GLY A 96 52 10.89 CISPEP 53 GLY A 95 GLY A 96 53 7.08 CISPEP 54 GLY A 95 GLY A 96 54 11.54 CISPEP 55 GLY A 95 GLY A 96 55 5.80 CISPEP 56 GLY A 95 GLY A 96 56 7.83 CISPEP 57 GLY A 95 GLY A 96 57 11.05 CISPEP 58 GLY A 95 GLY A 96 58 7.68 CISPEP 59 GLY A 95 GLY A 96 59 9.27 CISPEP 60 GLY A 95 GLY A 96 60 5.53 CISPEP 61 GLY A 95 GLY A 96 61 6.42 CISPEP 62 GLY A 95 GLY A 96 62 7.35 CISPEP 63 GLY A 95 GLY A 96 63 9.31 CISPEP 64 GLY A 95 GLY A 96 64 14.45 CISPEP 65 GLY A 95 GLY A 96 65 11.62 CISPEP 66 GLY A 95 GLY A 96 66 11.02 CISPEP 67 GLY A 95 GLY A 96 67 7.68 CISPEP 68 GLY A 95 GLY A 96 68 6.90 CISPEP 69 GLY A 95 GLY A 96 69 9.21 CISPEP 70 GLY A 95 GLY A 96 70 9.62 CISPEP 71 GLY A 95 GLY A 96 71 7.88 CISPEP 72 GLY A 95 GLY A 96 72 4.04 CISPEP 73 GLY A 95 GLY A 96 73 4.47 CISPEP 74 GLY A 95 GLY A 96 74 5.59 CISPEP 75 GLY A 95 GLY A 96 75 5.87 CISPEP 76 GLY A 95 GLY A 96 76 9.78 CISPEP 77 GLY A 95 GLY A 96 77 5.28 CISPEP 78 GLY A 95 GLY A 96 78 9.81 CISPEP 79 GLY A 95 GLY A 96 79 5.09 CISPEP 80 GLY A 95 GLY A 96 80 2.49 SITE 1 AC1 14 ILE A 5 ALA A 6 ALA A 7 ASP A 27 SITE 2 AC1 14 PHE A 31 LYS A 32 ILE A 50 ARG A 57 SITE 3 AC1 14 ILE A 94 THR A 113 NAP A 202 HOH A 316 SITE 4 AC1 14 HOH A 333 HOH A 335 SITE 1 AC2 29 ALA A 6 ALA A 7 ILE A 14 GLY A 15 SITE 2 AC2 29 ASN A 18 ALA A 19 GLY A 43 ARG A 44 SITE 3 AC2 29 HIS A 45 THR A 46 LEU A 62 SER A 63 SITE 4 AC2 29 SER A 64 LYS A 76 ILE A 94 GLY A 96 SITE 5 AC2 29 GLY A 97 ARG A 98 VAL A 99 TYR A 100 SITE 6 AC2 29 GLN A 102 ASP A 131 FOL A 201 HOH A 315 SITE 7 AC2 29 HOH A 321 HOH A 326 HOH A 330 HOH A 344 SITE 8 AC2 29 HOH A 346 CRYST1 34.102 45.595 99.113 90.00 90.00 90.00 P 21 21 21 4 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 0.029324 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010089 0.00000