1J5G - Header Asymmetric Unit

HEADER GENE REGULATION/DNA 03-MAY-02 1J5G

TITLE KNOWLEDGE BASED MODEL OF A LAMBDA REPRESSOR TETRAMER (TWO TITLE 2 DIMERS) BOUND TO TWO ADJACENT OPERATOR SITES

COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOPHAGE LAMBDA REPRESSOR CI RESIDUES 1-236; COMPND 3 CHAIN: A, B, C, D; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: DNA (44 NUCLEOTIDES OPERATOR SITE); COMPND 6 CHAIN: E; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: DNA (44 NUCLEOTIDES OPERATOR SITE); COMPND 10 CHAIN: F; COMPND 11 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE LAMBDA; SOURCE 3 ORGANISM_COMMON: VIRUS; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 3; SOURCE 7 SYNTHETIC: YES

KEYWDS FULL LAMBDA REPRESSOR, GENE REGULATION, OPERATOR SITES, KEYWDS 2 PROTEIN/DNA

EXPDTA THEORETICAL MODEL

AUTHOR R.CHATTOPADHYAYA,K.GHOSH

REVDAT 2 01-APR-03 1J5G 1 JRNL REVDAT 1 13-MAY-02 1J5G 0

SPRSDE 13-MAY-02 1J5G 1LMD

JRNL AUTH K.GHOSH,R.CHATTOPADHYAYA JRNL TITL PAPAIN DOES NOT CLEAVE OPERATOR-BOUND LAMBDA JRNL TITL 2 REPRESSOR: STRUCTURAL CHARACTERIZATION OF THE JRNL TITL 3 CARBOXY TERMINAL DOMAIN AND THE HINGE. JRNL REF J.BIOMOL.STRUCT.DYN. V. 18 557 2001 JRNL REFN ASTM JBSDD6 US ISSN 0739-1102

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.J.BEAMER,C.O.PABO REMARK 1 TITL REFINED 1.8A CRYSTAL STRUCTURE OF THE LAMBDA REMARK 1 TITL 2 REPRESSOR-OPERATOR COMPLEX REMARK 1 REF J.MOL.BIOL. V. 227 177 1992 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.O.PABO,M.LEWIS REMARK 1 TITL THE OPERATOR-BINDING DOMAIN OF LAMBDA REPRESSOR : REMARK 1 TITL 2 STRUCTURE AND DNA RECOGNITION REMARK 1 REF NATURE V. 298 443 1982 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.T.SAUER,R.R.YOCUM,R.F.DOOLITTLE,M.LEWIS,C.O.PABO REMARK 1 TITL HOMOLOGY AMONG DNA-BINDING PROTEINS SUGGESTS USE REMARK 1 TITL 2 OF A CONSERVED SUPER- SECONDARY STRUCTURE REMARK 1 REF NATURE V. 298 447 1982 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.T.SAUER,S.R.JORDAN,C.O.PABO REMARK 1 TITL LAMBDA REPRESSOR : A MODEL SYSTEM FOR REMARK 1 TITL 2 UNDERSTANDING PROTEIN-DNA INTERACTIONS AND PROTEIN REMARK 1 TITL 3 STABILITY REMARK 1 REF ADV.PROTEIN CHEM. V. 40 1 1990 REMARK 1 REFN ASTM APCHA2 US ISSN 0065-3233 REMARK 1 REFERENCE 5 REMARK 1 AUTH U.BANIK,R.SAHA,N.C.MANDAL,B.BHATTACHARYYA,S.ROY REMARK 1 TITL MULTIPHASIC DENATURATION OF THE LAMBDA REPRESSOR REMARK 1 TITL 2 BY UREA AND ITS IMPLICATIONS FOR THE REPRESSOR REMARK 1 TITL 3 STRUCTURE REMARK 1 REF EUR.J.BIOCHEM. V. 206 15 1992 REMARK 1 REFN ASTM EJBCAI IX ISSN 0014-2956 REMARK 1 REFERENCE 6 REMARK 1 AUTH A.D.JOHNSON,A.R.POTEETE,G.LAUER,R.T.SAUER, REMARK 1 AUTH 2 G.K.ACKERS,M.PTASHNE REMARK 1 TITL LAMBDA REPRESSOR AND CRO COMPONENTS OF AN REMARK 1 TITL 2 EFFICIENT MOLECULAR SWITCH REMARK 1 REF NATURE V. 294 217 1981 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 7 REMARK 1 AUTH F.W.WHIPPLE,N.H.KULDELL,L.A.CHEATHAM,A.HOCHSCHILD REMARK 1 TITL SPECIFICITY DETERMINANTS FOR THE INTERACTION OF REMARK 1 TITL 2 LAMBDA REPRESSOR AND P22 REPRESSOR DIMERS REMARK 1 REF GENES DEV. V. 8 1212 1994 REMARK 1 REFN ASTM GEDEEP US ISSN 0890-9369 REMARK 1 REFERENCE 8 REMARK 1 AUTH D.N.WOOLFSON,P.E.EVANS,E.G.HUTCHINSON,J.M.THORNTON REMARK 1 TITL TOPOLOGICAL AND STEREOCHEMICAL RESTRICTIONS IN REMARK 1 TITL 2 BETA-SANDWICH PROTEIN STRUCTURES REMARK 1 REF PROTEIN ENG. V. 6 461 1993 REMARK 1 REFN ASTM PRENE9 UK ISSN 0269-2139 REMARK 1 REFERENCE 9 REMARK 1 AUTH D.S.BURZ,G.K.ACKERS REMARK 1 TITL SELF-ASSEMBLY OF BACTERIOPHAGE LAMBDA CI REPRESSOR REMARK 1 TITL 2 EFFECTS OF SINGLE-SITE MUTATIONS ON THE REMARK 1 TITL 3 MONOMER-DIM EQUILIBRIUM REMARK 1 REF BIOCHEMISTRY V. 33 8399 1994 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 10 REMARK 1 AUTH D.S.BURZ,G.K.ACKERS REMARK 1 TITL SINGLE-SITE MUTATIONS IN THE C-TERMINAL DOMAIN OF REMARK 1 TITL 2 BACTERIOPHAGE LAMBDA CI REPRESSOR ALTER REMARK 1 TITL 3 COOPERATIVE INTERACTIONS BETWEEN DIMERS ADJACENTLY REMARK 1 TITL 4 BOUND TO OR REMARK 1 REF BIOCHEMISTRY V. 33 8406 1994 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 11 REMARK 1 AUTH K.S.KOBLAN,G.K.ACKERS REMARK 1 TITL ENERGETICS OF SUBUNIT DIMERIZATION IN REMARK 1 TITL 2 BACTERIOPHAGE LAMBDA CI REPRESSOR : LINKAGE TO REMARK 1 TITL 3 PROTONS, TEMPERATURE AND KCL REMARK 1 REF BIOCHEMISTRY V. 30 7817 1991 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 12 REMARK 1 AUTH K.S.KOBLAN,G.K.ACKERS REMARK 1 TITL COOPERATIVE PROTEIN-DNA INTERACTIONS : EFFECTS OF REMARK 1 TITL 2 KCL ON LAMBDA CI BINDING TO OR REMARK 1 REF BIOCHEMISTRY V. 30 7822 1991 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 13 REMARK 1 AUTH D.STRAHS,M.BRENOWITZ REMARK 1 TITL DNA CONFORMATIONAL CHANGES ASSOCIATED WITH THE REMARK 1 TITL 2 COOPERATIVE BINDING OF CI- REPRESSOR OF REMARK 1 TITL 3 BACTERIOPHAGE LAMBDA TO OR REMARK 1 REF J.MOL.BIOL. V. 244 494 1994 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 14 REMARK 1 AUTH J.W.LITTLE REMARK 1 TITL AUTODIGESTION OF LEXA AND PHAGE LAMBDA REPRESSORS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 81 1375 1984 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 15 REMARK 1 AUTH V.I.LIM REMARK 1 TITL STRUCTURAL PRINCIPLES OF THE GLOBULAR ORGANIZATION REMARK 1 TITL 2 OF PROTEIN CHAINS. A STEREOCHEMICAL THEORY OF REMARK 1 TITL 3 GLOBULAR PROTEIN STRUCTURE REMARK 1 REF J.MOL.BIOL. V. 88 857 1974 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 16 REMARK 1 AUTH G.GHOSH,G.VAN DUYNE,S.GHOSH,P.B.SIGLER REMARK 1 TITL STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE REMARK 1 REF NATURE V. 373 303 1995 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 17 REMARK 1 AUTH A.L.DONNER,P.A.CARLSON,G.B.KOUDELKA REMARK 1 TITL DIMERIZATION SPECIFICITY OF P22 AND 434 REPRESSORS REMARK 1 TITL 2 IS DETERMINED BY MULTIPLE POLYPEPTIDE SEGMENTS REMARK 1 REF J.BACTERIOL. V. 179 1253 1997 REMARK 1 REFN ASTM JOBAAY US ISSN 0021-9193 REMARK 1 REFERENCE 18 REMARK 1 AUTH T.S.PEAT,E.G.FRANK,J.P.MCDONALD,A.S.LEVINE, REMARK 1 AUTH 2 R.WOODGATE,W.A.HENDRICKSON REMARK 1 TITL STRUCTURE OF THE UMUD' PROTEIN AND ITS REGULATION REMARK 1 TITL 2 IN RESPONSE TO DNA DAMAGE REMARK 1 REF NATURE V. 380 727 1996 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1J5G COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PRAGUE ON 09-MAY-2002. REMARK 100 THE RCSB ID CODE IS RCSB001635.

REMARK 102 REMARK 102 BASES G E 25 AND A F 66 ARE MISPAIRED.

REMARK 103 REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE REMARK 103 FOLLOWING ATOMS: REMARK 103 N1 A E 4 AND N3 T F 86 REMARK 103 N1 G E 17 AND N3 C F 73 REMARK 103 N3 T E 18 AND N1 A F 72 REMARK 103 N1 G E 25 AND N1 A F 66 REMARK 103 N1 A E 26 AND N3 T F 64 REMARK 103 N3 T E 27 AND N1 A F 63 REMARK 103 N1 A E 28 AND N3 T F 62 REMARK 103 N3 T E 39 AND N1 A F 51 REMARK 103 N3 T E 42 AND N1 A F 48

REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: MODEL BUILDING FOR THE COMPLETE LAMBDA REPRESSOR REMARK 220 TETRAMER AND ASSOCIATED OPERATOR DNA WAS CARRIED OUT REMARK 220 USING THE INSIGHT-II PACKAGE INCLUDING PROGRAMS DISCOVER REMARK 220 AND HOMOLOGY

REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.

REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE BACTERIOPHAGE LAMBDA CI REPRESSOR IS A TWO DOMAIN, REMARK 400 236 RESIDUE REGULATORY PROTEIN. THE N-DOMAIN (1-92) REMARK 400 BINDS DNA, WHILE THE C-DOMAIN (93-236) IS INVOLVED IN REMARK 400 PROTEIN-PROTEIN CONTACTS. THE CI REPRESSOR BINDS TWO REMARK 400 SETS OF THREE HOMOLOGOUS, PARTIALLY SYMMETRIC BINDING REMARK 400 SITES (OR1,OR2,OR3,OL1,OL2,OL3) KNOWN AS OPERATOR REMARK 400 SITES. AT EACH OPERATOR SITE, A DIMER OF THE REPRESSOR REMARK 400 BINDS (REF.6 ABOVE). REMARK 400 REMARK 400 THE CRYSTAL STRUCTURES OF THE N-DOMAIN (1-92; REF. 2 REMARK 400 ABOVE; PDB CODE 1LRP) AND THE N-DOMAIN COMPLEXED WITH REMARK 400 THE OL1 OPERATOR SITE (REF.1 ABOVE; PDB CODE 1LMB) ARE REMARK 400 AVAILABLE. HOWEVER, THE INTACT CI REPRESSOR OR ITS REMARK 400 COMPLEX WITH OPERATOR DNA COULD NOT BE CRYSTALLIZED REMARK 400 YET, THOUGH THE CRYSTAL STRUCTURE OF FRAGMENT 132-236 REMARK 400 WAS REPORTED IN JUNE 2000 (REF.20 ABOVE), ALMOST REMARK 400 SIMULTANEOUSLY WITH A COMPARATIVE MODEL OF THE REMARK 400 LAMBDA REPRESSOR TETRAMER IN PDB ENTRY 1GFX. THE RMS REMARK 400 DIFFERENCE BETWEEN RESIDUES 138-236 IN 1GFX (RELEASED REMARK 400 JULY 3, 2000) AND THE CRYSTAL STRUCTURE IN 1F39 REMARK 400 (RELEASED JULY 26, 2000) IS 1.24 ANGSTROMS IN MAIN REMARK 400 CHAIN ATOMS. OUR ORIGINAL AB INITIO MODEL IN 1LMD REMARK 400 PROVED TO BE INCORRECT IN LIGHT OF THE CRYSTAL REMARK 400 STRUCTURE, HOWEVER, MANY FEATURES OF IT WERE CORRECT. REMARK 400 REMARK 400 ORIGINALLY WE SUBMITTED AN AB INITIO MODEL IN 1LMD REMARK 400 USING SECONDARY STRUCTURE PREDICTION, CD SPECTRA, AND REMARK 400 UNREACTIVITY OF THE THREE CYSTEINES AT RESIDUES 180, REMARK 400 215, 219 AND PROXIMITY OF THE AUTOCLEAVAGE CATALYTIC REMARK 400 AND SUBSTRATE RESIDUES TO ARRIVE AT A JELLY ROLL FOLD. REMARK 400 REMARK 400 UNLIKE IN THE CASE OF LEXA (REF.19) INITIALLY WE HAD REMARK 400 RULED OUT THE UMUD' FOLD FOR THE LAMBDA REPRESSOR REMARK 400 BASED ON AN AMINO ACID ALIGNMENT OF HOMOLOGOUS PROTEINS REMARK 400 GIVEN IN REF.18 ABOVE, SHOWING CYS 215 AND 219 WITH REMARK 400 EXPOSED SIDE CHAINS, REMARK 400 WHEREAS EXPERIMENT SHOWED NO REACTION OF CYSTEINES REMARK 400 WITH DTNB (REF.19). HOWEVER, WE LATER REALIZED THAT REMARK 400 ONE COULD KEEP THE UMUD' FOLD AND JUST CHANGE THE REMARK 400 LOCAL ALIGNMENT NEAR THE CYSTEINES 215 AND 219 SO REMARK 400 THAT THEY BECAME BURIED IN THE PROTEIN STRUCTURE, REMARK 400 AND THIS RESULTED IN ENTRY 1GFX. REMARK 400 REMARK 400 THE PRESENT ENTRY IS IDENTICAL TO 1GFX AS FAR AS THE REMARK 400 OPERATOR DNA STRUCTURE, N-DOMAINS AND C-DOMAINS ARE REMARK 400 CONCERNED. HOWEVER, THE N-C CONNECTIVITY IS DIFFERENT REMARK 400 AND THE LINKER REGION HERE IS PARTIALLY BASED ON THE REMARK 400 CLEAVAGE SITE IN THE LEXA CRYSTAL STRUCTURE 1JHH. REMARK 400 AS WITH OUR MODEL FOR LEXA IN 1QAA, WE KEPT THE REMARK 400 CLEAVAGE SITE NEAR THE CATALYTIC SITE. THIS IS IN REMARK 400 AGREEMENT WITH OUR DATA THAT PH-DEPENDENT AUTOCLEAVAGE REMARK 400 OF THE LAMBDA REPRESSOR IS ACTUALLY SPEEDED BY BINDING REMARK 400 TO THE OPERATOR DNA. REMARK 400 REMARK 400 UNLIKE 1GFX, THE PRESENT MODEL REPRESENTS A SWAP REMARK 400 MODEL WITHIN A REPRESSOR DIMER, THAT IS, THE C-DOMAIN REMARK 400 SITS ON TOP OF THE N-DOMAIN FROM THE OTHER OPERATOR REMARK 400 HALF SITE. ACCORDINGLY, IF MOLECULES A,B,C,D ARE IN REMARK 400 AN ORDER BY THEIR BINDING TO TWO OPERATOR SITES IN REMARK 400 THE SAME DIRECTION, MOLECULES A AND D FORM THE REMARK 400 COOPERATIVE CONTACT IN THE PRESENT MODEL, WHEREAS REMARK 400 IN 1GFX, MOLECULES B AND C DO. REMARK 400 REMARK 400 WE HAVE USED THE PDB ENTRY 1LMB TO MODEL THE OPERATOR REMARK 400 SITES AND THE ATTACHED N-DOMAINS. HENCE RESIDUES 1-92 REMARK 400 IN OUR MODEL POSSESS AN IDENTICAL STRUCTURE TO THIS REMARK 400 CRYSTAL STRUCTURE. OUR MODEL CONTAINS TWO SUCH DIMERS REMARK 400 WITH SOME INTERVENING BASE PAIRS CORRESPONDING TO THE REMARK 400 REGION BETWEEN OR1 AND OR2 SITES. REGION 151-160 REMARK 400 FROM PDB ENTRY 1F39 HAS BEEN USED IN THIS PRESENT REMARK 400 MODEL SINCE THIS LOOP WAS CONSTANT AMONG MANY REMARK 400 DIFFERENT STRUCTURES OF THE C-DOMAIN (REF.22) IN REMARK 400 DIFFERENT CRYSTALLINE ENVIRONMENTS. ALSO, REGION REMARK 400 105-118 IN THIS MODEL IS BASED ON THE CLEAVAGE SITE REMARK 400 FOUND IN THE RECENT CRYSTAL STRUCTURE OF LEXA (REF.21). REMARK 400 REMARK 400 CIRCULAR DICHROISM SPECTRA FOR THE VARIOUS PURIFIED REMARK 400 C-TERMINAL FRAGMENTS WERE RECORDED AND THEY TALLIED REMARK 400 WITH OUR SECONDARY STRUCTURE PREDICTIONS FOR THE REMARK 400 C-DOMAIN. AMOUNT OF HELIX CONTENT DECREASED AS THE REMARK 400 SIZE OF THE C-TERMINAL FRAGMENT DECREASED, WITH REMARK 400 THE FRAGMENT 132-236 SHOWING ALMOST PURE BETA REMARK 400 SHEET CD SPECTRUM. A TOTAL OF EIGHT BETA STRANDS REMARK 400 ARE PREDICTED IN THE REGION 93-236 BY OUR METHOD. REMARK 400 SUPPORTING DATA WERE OBTAINED BY FTIR (GHOSH AND REMARK 400 CHATTOPADHYAYA, 2001). REMARK 400 REMARK 400 THE VARIOUS MUTAGENESIS STUDIES (REFS.4,7,9,10 AND REMARK 400 MANY MORE) HELPED US TO BRING SPECIFIC RESIDUES OF REMARK 400 LAMBDA REPRESSOR ON THE EXTERIOR SURFACE, THUS REMARK 400 PROVIDING ADDITIONAL CHECKS FOR OUR MODEL. IN REMARK 400 ADDITION, DELINEATION OF THE MONOMER-MONOMER REMARK 400 INTERFACE AND THE DIMER-DIMER INTERFACE BECAME REMARK 400 POSSIBLE BY USING THESE BIOCHEMICAL DATA. THE REMARK 400 LAMBDA REPRESSOR DIMER FORMATION IS AKIN TO THE REMARK 400 NF-KB DIMER FORMATION (REF.16 ABOVE) IN THAT, THEY REMARK 400 BOTH USE HYDROPHOBIC SIDE CHAINS ON THE EXTERIOR REMARK 400 OF THEIR C-DOMAIN BETA BARRELS, FORMING A PSEUDO REMARK 400 BARREL AT THE MONOMER-MONOMER INTERFACE. WE ARE REMARK 400 PLEASANTLY SURPRISED WITH THE RECENT WORK OF REMARK 400 DONNER ET AL (REF.17) WHICH PREDICTS FROM AN REMARK 400 INDEPENDENT EXPERIMENTAL APPROACH THAT 434 REPRESSOR REMARK 400 USES THE VERY SAME REGIONS FOR DIMERIZATION THAT REMARK 400 WE HAVE ALREADY PREDICTED FROM ENTIRELY DIFFERENT REMARK 400 RESULTS FOR THE LAMBDA CI REPRESSOR. REMARK 400 REMARK 400 IN OUR MODEL, THE REGION 195-210 CONTAINING BETA6 REMARK 400 AND TWO ADJACENT LOOPS ARE MOST CRUCIAL FOR THE REMARK 400 COOPERATIVE OR DIMER-DIMER INTERACTIONS. REMARK 400 THE P22 AND 434 REPRESSOR C-DOMAINS ARE REMARK 400 GENERATED BY HOMOLOGY STARTING FROM THE FINAL REMARK 400 LAMBDA REPRESSOR C-DOMAIN, BUT THEIR CONNECTIVITIES REMARK 400 WITH THEIR RESPECTIVE N-DOMAINS ARE DIFFERENT REMARK 400 WHEN COMPARED TO THE LAMBDA REPRESSOR. REMARK 400 REMARK 400 1 44 REMARK 400 5'-TATATCACCGCCAGTGGTATTTATGATATCACCGCCAGTGGTAT-3' REMARK 400 3'-TATAGTGGCGGTCACCATAAATACTATAGTGGCGGTCACCATAA-5' REMARK 400 88 45 REMARK 400 REMARK 400 THE CRYSTAL STRUCTURE 1LMB SHOWS A BEND OF ABOUT 16 REMARK 400 DEGREES IN THE HELIX AXIS IN OL1. SINCE WE HAVE TWO REMARK 400 OF THEM, ABOUT 30 DEGREES OF BENDING ARE DUE TO THE REMARK 400 TWO OL1 SITES IN THE ABOVE DNA MOLECULE. THE INTER REMARK 400 -VENING BASE PAIRS EXHIBIT AN AVERAGE TWIST OF 27 REMARK 400 DEGREES. WATSON-CRICK BASE PAIRING IS PRESERVED, REMARK 400 THOUGH DISTORTED IN SOME INTERVENING BASE PAIRS (21- REMARK 400 25) RISE PER STEP IS HIGHER THAN NORMAL AND AN REMARK 400 ADDITIONAL BEND OF 15 DEGREES IS SEEN. REMARK 400 REMARK 400 ATOMS ORIGINALLY TAKEN FROM 1LMB BEAR THEIR ORIGINAL REMARK 400 TEMPERATURE FACTORS AND CAN BE IDENTIFIED AS SUCH. REMARK 400 REMARK 400 THERE ARE FOUR LAMBDA REPRESSOR MOLECULES WITH CHAIN REMARK 400 IDENTIFIERS *A*,*B*,*C* AND *D* RESPECTIVELY. OPERATOR REMARK 400 DNA CHAIN IDENTIFIERS CONTAIN NUCLEOTIDE TYPE AND REMARK 400 SEQUENCE NUMBER FROM THE 5 PRIME END, NUMBER VARYING REMARK 400 FROM 1-44 AND 45-88 FOR THE TWO STRANDS. WATSON-CRICK REMARK 400 BASE PAIRING OCCURS BETWEEN 2-44 AND 46-88. REMARK 400

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 SER B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 LYS B 4 REMARK 465 LYS B 5 REMARK 465 SER D 1 REMARK 465 THR D 2 REMARK 465 LYS D 3 REMARK 465 LYS D 4 REMARK 465 LYS D 5

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O2P T F 83 N GLY A 43 1.79 REMARK 500 O2P T F 71 N GLN B 33 1.90 REMARK 500 O2P T E 27 N GLN C 33 1.93 REMARK 500 O2P A E 37 N ALA D 56 2.06 REMARK 500 O1P T F 71 OH TYR B 22 2.07 REMARK 500 O2P T E 39 CB MET D 42 2.13 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO D 211 CB - CA - C ANGL. DEV. = 22.4 DEGREES REMARK 500 PRO D 211 N - CA - CB ANGL. DEV. =-31.0 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 SER A 107 -168.76 111.74 REMARK 500 THR A 122 -94.99 74.44 REMARK 500 THR A 133 -87.92 62.49 REMARK 500 LYS A 134 -74.31 67.93 REMARK 500 ASP A 138 -46.56 71.12 REMARK 500 SER A 198 145.18 69.36 REMARK 500 GLN A 200 -83.06 66.10 REMARK 500 SER B 107 -168.71 115.14 REMARK 500 THR B 122 -96.03 75.23 REMARK 500 THR B 133 -87.90 62.51 REMARK 500 LYS B 134 -74.29 67.96 REMARK 500 ASP B 138 -46.86 70.85 REMARK 500 SER B 198 145.21 69.37 REMARK 500 GLN B 200 -83.07 66.11 REMARK 500 SER C 107 -168.72 127.30 REMARK 500 THR C 122 -90.64 76.40 REMARK 500 THR C 133 -87.88 62.38 REMARK 500 LYS C 134 -74.17 67.96 REMARK 500 ASP C 138 -45.04 71.01 REMARK 500 SER C 198 145.19 69.47 REMARK 500 GLN C 200 -83.03 65.98 REMARK 500 THR D 122 -92.10 74.23 REMARK 500 THR D 133 -87.79 62.44 REMARK 500 LYS D 134 -74.15 68.00 REMARK 500 ASP D 138 -45.64 71.68 REMARK 500 SER D 198 145.25 69.35 REMARK 500 GLN D 200 -83.15 66.12 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 MET A 113 PHE A 114 142.42 REMARK 500 MET B 113 PHE B 114 142.57 REMARK 500 PRO C 104 VAL C 105 -148.10 REMARK 500 MET C 113 PHE C 114 142.34 REMARK 500 GLU D 102 TYR D 103 -142.18 REMARK 500 PRO D 104 VAL D 105 -146.11 REMARK 500 GLN D 110 ALA D 111 141.46 REMARK 500 MET D 113 PHE D 114 144.70 REMARK 500 PRO D 208 GLN D 209 142.91

DBREF 1J5G A 1 236 UNP P03034 RPC1_LAMBD 1 236 DBREF 1J5G B 1 236 UNP P03034 RPC1_LAMBD 1 236 DBREF 1J5G C 1 236 UNP P03034 RPC1_LAMBD 1 236 DBREF 1J5G D 1 236 UNP P03034 RPC1_LAMBD 1 236

SEQRES 1 A 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 A 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 A 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 A 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 A 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 A 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 A 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 A 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 A 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 A 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 A 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 A 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 A 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 A 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 A 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 A 236 ARG ASP SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 A 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 A 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 A 236 PHE GLY SEQRES 1 B 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 B 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 B 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 B 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 B 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 B 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 B 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 B 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 B 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 B 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 B 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 B 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 B 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 B 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 B 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 B 236 ARG ASP SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 B 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 B 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 B 236 PHE GLY SEQRES 1 C 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 C 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 C 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 C 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 C 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 C 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 C 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 C 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 C 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 C 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 C 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 C 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 C 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 C 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 C 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 C 236 ARG ASP SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 C 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 C 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 C 236 PHE GLY SEQRES 1 D 236 SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU SEQRES 2 D 236 ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS SEQRES 3 D 236 ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS SEQRES 4 D 236 MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN SEQRES 5 D 236 GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU SEQRES 6 D 236 ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO SEQRES 7 D 236 SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL SEQRES 8 D 236 SER MET GLN PRO SER LEU ARG SER GLU TYR GLU TYR PRO SEQRES 9 D 236 VAL PHE SER HIS VAL GLN ALA GLY MET PHE SER PRO GLU SEQRES 10 D 236 LEU ARG THR PHE THR LYS GLY ASP ALA GLU ARG TRP VAL SEQRES 11 D 236 SER THR THR LYS LYS ALA SER ASP SER ALA PHE TRP LEU SEQRES 12 D 236 GLU VAL GLU GLY ASN SER MET THR ALA PRO THR GLY SER SEQRES 13 D 236 LYS PRO SER PHE PRO ASP GLY MET LEU ILE LEU VAL ASP SEQRES 14 D 236 PRO GLU GLN ALA VAL GLU PRO GLY ASP PHE CYS ILE ALA SEQRES 15 D 236 ARG LEU GLY GLY ASP GLU PHE THR PHE LYS LYS LEU ILE SEQRES 16 D 236 ARG ASP SER GLY GLN VAL PHE LEU GLN PRO LEU ASN PRO SEQRES 17 D 236 GLN TYR PRO MET ILE PRO CYS ASN GLU SER CYS SER VAL SEQRES 18 D 236 VAL GLY LYS VAL ILE ALA SER GLN TRP PRO GLU GLU THR SEQRES 19 D 236 PHE GLY SEQRES 1 E 44 T A T A T C A C C G C C A SEQRES 2 E 44 G T G G T A T T T A T G A SEQRES 3 E 44 T A T C A C C G C C A G T SEQRES 4 E 44 G G T A T SEQRES 1 F 44 A A T A C C A C T G G C G SEQRES 2 F 44 G T G A T A T C A T A A A SEQRES 3 F 44 T A C C A C T G G C G G T SEQRES 4 F 44 G A T A T

HELIX 1 1 THR A 8 GLY A 30 1 23 HELIX 2 2 SER A 32 GLY A 41 1 10 HELIX 3 3 GLY A 43 ASN A 52 1 10 HELIX 4 4 ASN A 58 LYS A 70 1 13 HELIX 5 5 SER A 72 PHE A 76 5 5 HELIX 6 6 SER A 77 MET A 93 1 17 HELIX 7 7 GLY A 124 THR A 132 1 9 HELIX 8 8 THR B 8 GLY B 30 1 23 HELIX 9 9 SER B 32 MET B 40 1 9 HELIX 10 10 GLY B 43 ASN B 52 1 10 HELIX 11 11 ASN B 58 LYS B 70 1 13 HELIX 12 12 SER B 72 PHE B 76 5 5 HELIX 13 13 SER B 77 MET B 93 1 17 HELIX 14 14 GLY B 124 THR B 132 1 9 HELIX 15 15 THR C 8 GLY C 30 1 23 HELIX 16 16 SER C 32 GLY C 41 1 10 HELIX 17 17 GLY C 43 ASN C 52 1 10 HELIX 18 18 ASN C 58 LYS C 70 1 13 HELIX 19 19 SER C 72 PHE C 76 5 5 HELIX 20 20 SER C 77 MET C 93 1 17 HELIX 21 21 ASP C 125 THR C 132 1 8 HELIX 22 22 THR D 8 GLY D 30 1 23 HELIX 23 23 SER D 32 MET D 40 1 9 HELIX 24 24 GLY D 43 ASN D 52 1 10 HELIX 25 25 ASN D 58 LYS D 70 1 13 HELIX 26 26 SER D 72 PHE D 76 5 5 HELIX 27 27 SER D 77 MET D 93 1 17 HELIX 28 28 ASP D 125 THR D 132 1 8

SHEET 1 A 3 HIS A 108 VAL A 109 0 SHEET 2 A 3 LYS A 192 LYS A 193 1 O LYS A 192 N VAL A 109 SHEET 3 A 3 VAL A 201 PHE A 202 -1 N VAL A 201 O LYS A 193 SHEET 1 B 3 LEU A 167 VAL A 168 0 SHEET 2 B 3 CYS A 180 ALA A 182 -1 O ILE A 181 N VAL A 168 SHEET 3 B 3 MET A 212 ILE A 213 -1 N ILE A 213 O CYS A 180 SHEET 1 C 3 HIS B 108 VAL B 109 0 SHEET 2 C 3 LYS B 192 LYS B 193 1 O LYS B 192 N VAL B 109 SHEET 3 C 3 VAL B 201 PHE B 202 -1 N VAL B 201 O LYS B 193 SHEET 1 D 3 LEU B 167 VAL B 168 0 SHEET 2 D 3 CYS B 180 ALA B 182 -1 O ILE B 181 N VAL B 168 SHEET 3 D 3 MET B 212 ILE B 213 -1 O ILE B 213 N CYS B 180 SHEET 1 E 3 HIS C 108 VAL C 109 0 SHEET 2 E 3 LYS C 192 LYS C 193 1 O LYS C 192 N VAL C 109 SHEET 3 E 3 VAL C 201 PHE C 202 -1 N VAL C 201 O LYS C 193 SHEET 1 F 3 LEU C 167 VAL C 168 0 SHEET 2 F 3 CYS C 180 ALA C 182 -1 O ILE C 181 N VAL C 168 SHEET 3 F 3 MET C 212 ILE C 213 -1 O ILE C 213 N CYS C 180 SHEET 1 G 3 HIS D 108 VAL D 109 0 SHEET 2 G 3 LYS D 192 LYS D 193 1 O LYS D 192 N VAL D 109 SHEET 3 G 3 VAL D 201 PHE D 202 -1 N VAL D 201 O LYS D 193 SHEET 1 H 3 LEU D 167 VAL D 168 0 SHEET 2 H 3 CYS D 180 ALA D 182 -1 O ILE D 181 N VAL D 168 SHEET 3 H 3 MET D 212 ILE D 213 -1 O ILE D 213 N CYS D 180

CISPEP 1 LYS A 157 PRO A 158 0 -1.15 CISPEP 2 LYS B 157 PRO B 158 0 -1.35 CISPEP 3 LYS C 157 PRO C 158 0 -1.47 CISPEP 4 LYS D 157 PRO D 158 0 -1.61

CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1

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 1.000000 0.000000 0.000000 0.00000

SCALE2 0.000000 1.000000 0.000000 0.00000

SCALE3 0.000000 0.000000 1.000000 0.00000