PDB Short entry for 5DFR HEADER OXIDOREDUCTASE 21-OCT-88 5DFR TITLE CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE TITLE 2 REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN TITLE 3 BINDING 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; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS OXIDO-REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.BYSTROFF,J.KRAUT REVDAT 4 06-MAR-24 5DFR 1 REMARK SEQADV REVDAT 3 29-NOV-17 5DFR 1 HELIX REVDAT 2 24-FEB-09 5DFR 1 VERSN REVDAT 1 15-JUL-90 5DFR 0 JRNL AUTH C.BYSTROFF,J.KRAUT JRNL TITL CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI JRNL TITL 2 DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL JRNL TITL 3 CHANGES AND COOPERATIVITY IN BINDING. JRNL REF BIOCHEMISTRY V. 30 2227 1991 JRNL REFN ISSN 0006-2960 JRNL PMID 1998681 JRNL DOI 10.1021/BI00222A028 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.BYSTROFF,S.J.OATLEY,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REMARK 1 TITL 2 REDUCTASE. THE NADP+ HOLOENZYME AND THE FOLATE(DOT)NADP+ REMARK 1 TITL 3 TERNARY COMPLEX. SUBSTRATE BINDING AND A MODEL FOR THE REMARK 1 TITL 4 TRANSITION STATE REMARK 1 REF BIOCHEMISTRY V. 29 3263 1990 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.T.BOLIN,D.J.FILMAN,D.A.MATTHEWS,R.C.HAMLIN,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS REMARK 1 TITL 2 CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS REMARK 1 TITL 3 RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE REMARK 1 REF J.BIOL.CHEM. V. 257 13650 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.M.PERRY,J.J.ONUFFER,N.A.TOUCHETTE,C.S.HERNDON, REMARK 1 AUTH 2 M.S.GITTELMAN,C.R.MATTHEWS,J.-T.CHEN,R.J.MAYER,K.TAIRA, REMARK 1 AUTH 3 S.J.BENKOVIC,E.E.HOWELL,J.KRAUT REMARK 1 TITL EFFECT OF SINGLE AMINO ACID REPLACEMENTS ON THE FOLDING AND REMARK 1 TITL 2 STABILITY OF DIHYDROFOLATE REDUCTASE FROM ESCHERICHIA COLI REMARK 1 REF BIOCHEMISTRY V. 26 2674 1987 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 4 REMARK 1 AUTH D.J.FILMAN,J.T.BOLIN,D.A.MATTHEWS,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS REMARK 1 TITL 2 CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS REMARK 1 TITL 3 RESOLUTION. II. ENVIRONMENT OF BOUND NADPH AND IMPLICATIONS REMARK 1 TITL 4 FOR CATALYSIS REMARK 1 REF J.BIOL.CHEM. V. 257 13663 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 5 REMARK 1 AUTH K.W.VOLZ,D.A.MATTHEWS,R.A.ALDEN,S.T.FREER,C.HANSCH, REMARK 1 AUTH 2 B.T.KAUFMAN,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURE OF AVIAN DIHYDROFOLATE REDUCTASE REMARK 1 TITL 2 CONTAINING PHENYLTRIAZINE AND NADPH REMARK 1 REF J.BIOL.CHEM. V. 257 2528 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 6 REMARK 1 AUTH D.A.MATTHEWS REMARK 1 TITL INTERPRETATION OF NUCLEAR MAGNETIC RESONANCE SPECTRA FOR REMARK 1 TITL 2 LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE BASED ON THE REMARK 1 TITL 3 X-RAY STRUCTURE OF THE ENZYME-METHOTREXATE-NADPH COMPLEX REMARK 1 REF BIOCHEMISTRY V. 18 1602 1979 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 7 REMARK 1 AUTH D.A.MATTHEWS,R.A.ALDEN,S.T.FREER,N.-H.XUONG,J.KRAUT REMARK 1 TITL DIHYDROFOLATE REDUCTASE FROM LACTOBACILLUS CASEI. REMARK 1 TITL 2 STEREOCHEMISTRY OF NADPH BINDING REMARK 1 REF J.BIOL.CHEM. V. 254 4144 1979 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 8 REMARK 1 AUTH M.POE,K.HOOGSTEEN,D.A.MATTHEWS REMARK 1 TITL PROTON MAGNETIC RESONANCE STUDIES ON ESCHERICHIA COLI REMARK 1 TITL 2 DIHYDROFOLATE REDUCTASE. ASSIGNMENT OF HISTIDINE C-2 PROTONS REMARK 1 TITL 3 IN BINARY COMPLEXES WITH FOLATES ON THE BASIS OF THE CRYSTAL REMARK 1 TITL 4 STRUCTURE WITH METHOTREXATE AND ON CHEMICAL MODIFICATIONS REMARK 1 REF J.BIOL.CHEM. V. 254 8143 1979 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 9 REMARK 1 AUTH D.A.MATTHEWS,R.A.ALDEN,J.T.BOLIN,D.J.FILMAN,S.T.FREER, REMARK 1 AUTH 2 R.HAMLIN,W.G.J.HOL,R.L.KISLIUK,E.J.PASTORE,L.T.PLANTE, REMARK 1 AUTH 3 N.-H.XUONG,J.KRAUT REMARK 1 TITL DIHYDROFOLATE REDUCTASE FROM LACTOBACILLUS CASEI. X-RAY REMARK 1 TITL 2 STRUCTURE OF THE ENZYME-METHOTREXATE-NADPH COMPLEX REMARK 1 REF J.BIOL.CHEM. V. 253 6946 1978 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 10 REMARK 1 AUTH C.D.BENNETT,J.A.RODKEY,J.M.SONDEY,R.HIRSCHMANN REMARK 1 TITL DIHYDROFOLATE REDUCTASE. THE AMINO ACID SEQUENCE OF THE REMARK 1 TITL 2 ENZYME FROM A METHOTREXATE-RESISTANT MUTANT OF ESCHERICHIA REMARK 1 TITL 3 COLI REMARK 1 REF BIOCHEMISTRY V. 17 1328 1978 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 11 REMARK 1 AUTH D.A.MATTHEWS,R.A.ALDEN,J.T.BOLIN,S.T.FREER,R.HAMLIN,N.XUONG, REMARK 1 AUTH 2 J.KRAUT,M.POE,M.WILLIAMS,K.HOOGSTEEN REMARK 1 TITL DIHYDROFOLATE REDUCTASE. X-RAY STRUCTURE OF THE BINARY REMARK 1 TITL 2 COMPLEX WITH METHOTREXATE REMARK 1 REF SCIENCE V. 197 452 1977 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 12 REMARK 1 AUTH M.POE,N.J.GREENFIELD,J.M.HIRSHFIELD,M.N.WILLIAMS,K.HOOGSTEEN REMARK 1 TITL DIHYDROFOLATE REDUCTASE. PURIFICATION AND CHARACTERIZATION REMARK 1 TITL 2 OF THE ENZYME FROM AN AMETHOPTERIN-RESISTANT MUTANT OF REMARK 1 TITL 3 ESCHERICHIA COLI REMARK 1 REF BIOCHEMISTRY V. 11 1023 1972 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1220 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 120 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.026 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.066 ; 0.035 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.077 ; 0.045 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.024 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.347 ; 0.200 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.229 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.235 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.213 ; 0.300 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 11.300; 5.000 REMARK 3 STAGGERED (DEGREES) : 26.500; 15.000 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.412 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.832 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.088 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.914 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE PAPER CITED ON THE *JRNL* RECORDS ABOVE DISCUSSES THE REMARK 3 QUESTION AS TO WHETHER THE PEPTIDE BOND BETWEEN GLY 95 AND REMARK 3 GLY 96 IS IN THE CIS OR THE TRANS CONFORMATION. REMARK 3 A DISORDERED MODEL IN WHICH THIS PEPTIDE EXISTS IN BOTH REMARK 3 CONFORMERS CANNOT BE RULED OUT. IN THIS ENTRY, HOWEVER, REMARK 3 ONLY COORDINATES CORRESPONDING TO THE TRANS CONFORMATION REMARK 3 ARE PROVIDED. REMARK 3 REMARK 3 RESIDUES PRO 21 - LEU 24 ARE WEAK. THERE IS UNINTERPRETED REMARK 3 DENSITY ASSOCIATED WITH THE SIDE CHAIN OF PHE 31. RESIDUES REMARK 3 GLY 95 - GLY 96 ARE PARTIALLY DISORDERED. VAL 10, GLU 120, REMARK 3 ASP 122, AND ASP 127 HAVE DISORDERED SIDE CHAINS. THE SIDE REMARK 3 CHAIN OF LEU 28, IN THE SUBSTRATE BINDING SITE, APPEARS TO REMARK 3 BE PARTIALLY DISORDERED. REMARK 4 REMARK 4 5DFR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000179695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 27.78333 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 55.56667 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 55.56667 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 27.78333 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 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 16 REMARK 465 GLU A 17 REMARK 465 ASN A 18 REMARK 465 ALA A 19 REMARK 465 MET A 20 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 120 CD OE1 OE2 REMARK 470 ASP A 122 CB CG OD1 OD2 REMARK 470 ASP A 127 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N LEU A 24 O HOH A 426 2.01 REMARK 500 O HOH A 348 O HOH A 389 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 90 CD GLU A 90 OE2 -0.089 REMARK 500 GLY A 97 N GLY A 97 CA 0.190 REMARK 500 TYR A 111 CG TYR A 111 CD2 -0.086 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 MET A 1 N - CA - CB ANGL. DEV. = -11.2 DEGREES REMARK 500 MET A 1 CG - SD - CE ANGL. DEV. = -11.0 DEGREES REMARK 500 TRP A 22 CB - CA - C ANGL. DEV. = 14.7 DEGREES REMARK 500 TRP A 22 N - CA - CB ANGL. DEV. = -13.8 DEGREES REMARK 500 LEU A 24 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 LEU A 28 CA - C - N ANGL. DEV. = 14.3 DEGREES REMARK 500 LEU A 28 O - C - N ANGL. DEV. = -11.7 DEGREES REMARK 500 LEU A 36 CB - CA - C ANGL. DEV. = 11.9 DEGREES REMARK 500 ARG A 44 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 TRP A 47 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 GLU A 48 CG - CD - OE2 ANGL. DEV. = -12.7 DEGREES REMARK 500 GLN A 65 CB - CA - C ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP A 69 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 70 CB - CG - OD1 ANGL. DEV. = 11.9 DEGREES REMARK 500 ASP A 70 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 70 O - C - N ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG A 71 CD - NE - CZ ANGL. DEV. = 13.4 DEGREES REMARK 500 ARG A 71 NH1 - CZ - NH2 ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 71 NE - CZ - NH2 ANGL. DEV. = -13.0 DEGREES REMARK 500 THR A 73 CA - CB - CG2 ANGL. DEV. = 11.8 DEGREES REMARK 500 GLU A 80 CA - CB - CG ANGL. DEV. = 20.8 DEGREES REMARK 500 GLU A 80 OE1 - CD - OE2 ANGL. DEV. = -9.3 DEGREES REMARK 500 GLU A 80 CG - CD - OE1 ANGL. DEV. = 13.7 DEGREES REMARK 500 ALA A 83 N - CA - CB ANGL. DEV. = -9.5 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 GLU A 90 OE1 - CD - OE2 ANGL. DEV. = -8.7 DEGREES REMARK 500 GLU A 90 CG - CD - OE1 ANGL. DEV. = 15.1 DEGREES REMARK 500 GLY A 95 N - CA - C ANGL. DEV. = 21.5 DEGREES REMARK 500 GLY A 95 CA - C - N ANGL. DEV. = -12.1 DEGREES REMARK 500 GLY A 96 CA - C - O ANGL. DEV. = -12.4 DEGREES REMARK 500 GLY A 97 C - N - CA ANGL. DEV. = -17.1 DEGREES REMARK 500 GLY A 97 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 TYR A 100 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 LEU A 112 O - C - N ANGL. DEV. = 10.7 DEGREES REMARK 500 HIS A 114 N - CA - CB ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP A 116 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 ALA A 117 CB - CA - C ANGL. DEV. = 9.3 DEGREES REMARK 500 ASP A 131 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 TRP A 133 O - C - N ANGL. DEV. = 9.7 DEGREES REMARK 500 PHE A 137 CG - CD1 - CE1 ANGL. DEV. = 6.7 DEGREES REMARK 500 PHE A 137 CD1 - CE1 - CZ ANGL. DEV. = -7.7 DEGREES REMARK 500 SER A 138 CB - CA - C ANGL. DEV. = -11.4 DEGREES REMARK 500 SER A 138 N - CA - CB ANGL. DEV. = -10.4 DEGREES REMARK 500 ASP A 142 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ALA A 145 CB - CA - C ANGL. DEV. = 14.1 DEGREES REMARK 500 SER A 150 CA - CB - OG ANGL. DEV. = -18.8 DEGREES REMARK 500 TYR A 151 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 GLU A 157 OE1 - CD - OE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 52 ANGLE DEVIATIONS. 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 ASP A 11 1.19 89.13 REMARK 500 THR A 68 44.72 -140.60 REMARK 500 ASP A 69 111.98 -165.10 REMARK 500 ASP A 87 79.92 -117.89 REMARK 500 PRO A 130 -49.23 -29.77 REMARK 500 ASP A 131 6.00 -69.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 12 0.21 SIDE CHAIN REMARK 500 ARG A 33 0.24 SIDE CHAIN REMARK 500 ARG A 44 0.29 SIDE CHAIN REMARK 500 ARG A 52 0.13 SIDE CHAIN REMARK 500 ARG A 57 0.13 SIDE CHAIN REMARK 500 ARG A 98 0.20 SIDE CHAIN REMARK 500 ARG A 158 0.20 SIDE CHAIN REMARK 500 ARG A 159 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE A 137 -11.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE IDENTITY OF IONS 501 THROUGH 503 IS NOT DETERMINED. THEY HAVE REMARK 600 TENATIVELY BEEN ASSIGNED AS CHLORINE IONS BASED ON THEIR ELECTRON REMARK 600 DENSITY, THE BINDING ENVIRONMENT, AND THE BELIEF THAT CHLORIDE IS REMARK 600 THE ONLY NEGATIVELY-CHARGED MONO-ATOMIC ION PRESENT IN THE REMARK 600 CRYSTALLIZATION MIXTURE. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 503 DBREF 5DFR A 1 159 UNP P0ABQ4 DYR_ECOLI 1 159 SEQADV 5DFR 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 CL A 501 1 HET CL A 502 1 HET CL A 503 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 3(CL 1-) FORMUL 5 HOH *120(H2 O) HELIX 1 HB LEU A 24 THR A 35 1 12 HELIX 2 HC GLY A 43 ILE A 50 1 8 HELIX 3 HE SER A 77 GLY A 86 1 10 HELIX 4 HF GLY A 96 LEU A 104 1 9 SHEET 1 S1 8 THR A 73 VAL A 75 0 SHEET 2 S1 8 LYS A 58 SER A 63 1 O ASN A 59 N THR A 73 SHEET 3 S1 8 PRO A 39 GLY A 43 1 N VAL A 40 O LYS A 58 SHEET 4 S1 8 ILE A 91 GLY A 95 1 N MET A 92 O PRO A 39 SHEET 5 S1 8 MET A 1 LEU A 8 1 O MET A 1 N ILE A 91 SHEET 6 S1 8 GLN A 108 ASP A 116 1 O LYS A 109 N LEU A 4 SHEET 7 S1 8 SER A 150 ARG A 159 -1 N ARG A 158 O GLN A 108 SHEET 8 S1 8 ASP A 132 HIS A 141 -1 N GLU A 134 O GLU A 157 SITE 1 AC1 4 LYS A 32 HOH A 338 HOH A 372 CL A 503 SITE 1 AC2 1 HIS A 114 SITE 1 AC3 2 HOH A 338 CL A 501 CRYST1 68.730 68.730 83.350 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 0.014550 0.008400 0.000000 0.00000 SCALE2 0.000000 0.016801 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011998 0.00000