1Z0L - Header Asymmetric Unit

HEADER TRANSCRIPTION/DNA 02-MAR-05 1Z0L

TITLE MODEL OF MYCOBACTERIOPHAGE L1 REPRESSOR DIMER BOUND TO ITS TITLE 2 COGNATE OPERATOR

CAVEAT 1Z0L THERE ARE CHIRALITY ERRORS AT THE CA CENTER OF LEU 21

COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPRESSOR-LIKE IMMUNITY PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GP71, L1 REPRESSOR; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'- COMPND 7 D(*TP*AP*TP*AP*GP*GP*TP*GP*GP*CP*TP*GP*TP*CP*AP*AP*GP*TP*AP COMPND 8 *T)-3'; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'- COMPND 13 D(*AP*AP*TP*AP*CP*TP*TP*GP*AP*CP*AP*GP*CP*CP*AP*CP*CP*TP*AP COMPND 14 *T)-3'; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIOPHAGE L5; SOURCE 3 ORGANISM_COMMON: VIRUSES; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 3; SOURCE 7 SYNTHETIC: YES

KEYWDS L1 REPRESSOR OPERATOR COMPLEX, LYSOGENY, TRANSCRIPTION KEYWDS 2 REGULATION, PROTEIN/DNA

EXPDTA THEORETICAL MODEL

AUTHOR R.CHATTOPADHYAYA,S.SAU

REVDAT 1 22-MAR-05 1Z0L 0

JRNL AUTH R.CHATTOPADHYAYA,T.GANGULY,S.SAU JRNL TITL MODEL OF L1 REPRESSOR DIMER BOUND TO ITS COGNATE JRNL TITL 2 OPERATOR JRNL REF TO BE PUBLISHED JRNL REFN

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.SAU,P.CHATTORAJ,T.GANGULY,C.Y.LEE,N.C.MANDAL REMARK 1 TITL CLONING AND SEQUENCING ANALYSIS OF THE REPRESSOR REMARK 1 TITL 2 GENE OF TEMPERATE MYCOBACTERIOPHAGE L1 REMARK 1 REF J.BIOCHEM.MOL.BIOL. V. 37 254 2004 REMARK 1 REFN KR ISSN 1225-8687 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.GANGULY,P.CHATTORAJ,M.DAS,P.K.CHANDA,N.C.MANDAL, REMARK 1 AUTH 2 C.Y.LEE,S.SAU REMARK 1 TITL A POINT MUTATION AT THE C-TERMINAL HALF OF THE REMARK 1 TITL 2 REPRESSOR OF TEMPERATE MYCOBACTERIOPHAGE L1 REMARK 1 TITL 3 AFFECTS ITS BINDING TO THE OPERATOR DNA REMARK 1 REF J.BIOCHEM.MOL.BIOL. V. 37 709 2004 REMARK 1 REFN KR ISSN 1225-8687 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.J.ZUCCOLA,D.J.FILMAN,D.M.COEN,J.M.HOGLE REMARK 1 TITL THE CRYSTAL STRUCTURE OF AN UNUSUAL PROCESSIVITY REMARK 1 TITL 2 FACTOR, HERPES SIMPLEX VIRUS UL42, BOUND TO THE C REMARK 1 TITL 3 TERMINUS OF ITS COGNATE POLYMERASE REMARK 1 REF MOL.CELL V. 5 267 2000 REMARK 1 REFN ASTM MOCEFL US ISSN 1097-2765 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.CHATTOPADHYAYA,K.GHOSH REMARK 1 TITL A COMPARATIVE THREE-DIMENSIONAL MODEL OF THE REMARK 1 TITL 2 CARBOXY-TERMINAL DOMAIN OF THE LAMBDA REPRESSOR REMARK 1 TITL 3 AND ITS USE TO BUILD INTACT REPRESSOR TETRAMER REMARK 1 TITL 4 MODELS BOUND TO ADJACENT OPERATOR SITES REMARK 1 REF J.STRUCT.BIOL. V. 141 103 2003 REMARK 1 REFN ASTM JSBIEM US ISSN 1047-8477 REMARK 1 REFERENCE 5 REMARK 1 AUTH R.CHATTOPADHYAYA,A.PAL REMARK 1 TITL IMPROVED MODEL OF A LEXA REPRESSOR DIMER BOUND TO REMARK 1 TITL 2 RECA OPERATOR REMARK 1 REF J.BIOMOL.STRUCT.DYN. V. 21 681 2004 REMARK 1 REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 1 REFERENCE 6 REMARK 1 AUTH S.N.SLILATY,J.A.RUPLEY,J.W.LITTLE REMARK 1 TITL INTRAMOLECULAR CLEAVAGE OF LEXA AND PHAGE LAMBDA REMARK 1 TITL 2 REPRESSORS: DEPENDENCE OF KINETICS ON REPRESSOR REMARK 1 TITL 3 CONCENTRATION, PH, TEMPERATURE, AND SOLVENT REMARK 1 REF BIOCHEMISTRY V. 25 6866 1986 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 7 REMARK 1 AUTH S.N.SLILATY,J.W.LITTLE REMARK 1 TITL LYSINE-156 AND SERINE-119 ARE REQUIRED FOR LEXA REMARK 1 TITL 2 REPRESSOR CLEAVAGE: A POSSIBLE MECHANISM REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 84 3987 1987 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 8 REMARK 1 AUTH Y.LUO,R.A.PFUETZNER,S.MOSIMANN,M.PAETZEL,E.A.FREY, REMARK 1 AUTH 2 M.CHERNEY,B.KIM,J.W.LITTLE,N.C.STRYNADKA REMARK 1 TITL CRYSTAL STRUCTURE OF LEXA: A CONFORMATIONAL SWITCH REMARK 1 TITL 2 FOR REGULATION OF SELF-CLEAVAGE REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 106 585 2001 REMARK 1 REFN ASTM CELLB5 US ISSN 0092-8674 REMARK 1 REFERENCE 9 REMARK 1 AUTH K.L.BROWN,G.J.SARKIS,C.WADSWORTH,G.F.HATFULL REMARK 1 TITL TRANSCRIPTIONAL SILENCING BY THE MYCOBACTERIOPHAGE REMARK 1 TITL 2 L5 REPRESSOR REMARK 1 REF EMBO J. V. 16 5914 1997 REMARK 1 REFN ASTM EMJODG UK ISSN 0261-4189 REMARK 1 REFERENCE 10 REMARK 1 AUTH M.K.DONNELLY-WU,W.R.JACOBS,G.F.HATFULL REMARK 1 TITL SUPERINFECTION IMMUNITY OF MYCOBACTERIOPHAGE L5: REMARK 1 TITL 2 APPLICATIONS FOR GENETIC TRANSFORMATION OF REMARK 1 TITL 3 MYCOBACTERIA REMARK 1 REF MOL.MICROBIOL. V. 7 407 1993 REMARK 1 REFN ASTM MOMIEE UK ISSN 0950-382X REMARK 1 REFERENCE 11 REMARK 1 AUTH L.A.KELLEY,R.M.MACCALLUM,M.J.E.STERNBERG REMARK 1 TITL ENHANCED GENOME ANNOTATION USING STRUCTURAL REMARK 1 TITL 2 PROFILES IN THE PROGRAM 3D-PSSM REMARK 1 REF J.MOL.BIOL. V. 299 499 2000 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 12 REMARK 1 AUTH L.J.BEAMER,C.O.PABO REMARK 1 TITL REFINED 1.8 A 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1Z0L COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-2005. REMARK 100 THE RCSB ID CODE IS RCSB032146.

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: AMONG THE MYCOBACTERIOPHAGES, L5, BXB1, I13, MS6 AND REMARK 220 L1 HAVE BEEN STUDIED TO SOME EXTENT AT THE MOLECULAR REMARK 220 LEVEL. MYCOBACTERIOPHAGE L1, A SISTER HOMOIMMUNE PHAGE REMARK 220 OF L5, HAS A 50-KB DOUBLE-STRANDED DNA GENOME. THE REMARK 220 CLONING AND PRELIMINARY CHARACTERIZATION OF THE REMARK 220 REPRESSOR GENES OF L1 AND A TEMPERATURE SENSITIVE MUTANT REMARK 220 WERE CARRIED OUT (REF.1 ABOVE). A POINT MUTATION P131L REMARK 220 IN THE C-TERMINAL HALF OF THE 183-RESIDUE L1 REPRESSOR REMARK 220 WAS ALSO REPORTED RECENTLY (REF.2). IT WAS ALSO REMARK 220 SUGGESTED THAT THIS L1 MYCOBACTERIOPHAGE REPRESSOR REMARK 220 CONTAINS AN HELIX-TURN-HELIX MOTIF NEAR ITS N-TERMINUS REMARK 220 (REF.1). IN THE PRESENT WORK A FULL THREE DIMENSIONAL REMARK 220 MODEL OF THIS L1 REPRESSOR, IDENTICAL IN PRIMARY REMARK 220 SEQUENCE TO THE L5 REPRESSOR (REF.10) HAS BEEN REMARK 220 CONSTRUCTED, THE REASONING BEING BRIEFLY EXPLAINED REMARK 220 BELOW. STEP ONE. RECOGNITION OF INTERNAL SYMMETRY IN THE REMARK 220 OPERATOR BINDING SITES OF THE L5 REPRESSOR HAVING REMARK 220 IDENTICAL PRIMARY SEQUENCE AS THE L1 REPRESSOR (REF.10) REMARK 220 THE 24 DIFFERENT OPERATOR BINDING SITES FOUND IN THE 52- REMARK 220 KB L5 MYCOBACTERIOPHAGE GENOME WAS SHOWN TO CONSIST OF A REMARK 220 13-BASE PAIR CONSENSUS SEQUENCE : 5'-GGTGGCTGTCAAG-3' 3' REMARK 220 -CCACCGACAGTTC-5' IN REF.11, THERE IS NO REMARK REMARK 220 REGARDING THE INTERNAL SYMMETRY OF THIS CONSENSUS REMARK 220 SEQUENCE. WE DISCOVERED THE EXISTENCE OF A PSEUDO-TWO REMARK 220 FOLD CENTER OF SYMMETRY IN THIS CONSENSUS SEQUENCE, AT REMARK 220 THE CENTRAL T-A BASE PAIR. THE SYMMETRY IS PERFECT FOR REMARK 220 THE 1ST, 3RD AND 4TH ADJACENT BASE PAIRS FROM THE REMARK 220 CENTRAL T-A BASE PAIR. THE SYMMETRY IS BROKEN AT THE REMARK 220 REMAINING 3 BASE PAIRS, BUT PURINE-PYRIMIDINE SYMMETRY REMARK 220 EXISTS AT THE 2ND BASE PAIR FROM THE CENTER. STEP TWO. REMARK 220 DUE TO THIS PSEUDO-SYMMETRY IT IS LIKELY THAT THE REMARK 220 REPRESSOR WILL BIND TO THESE OPERATOR SITES AS A DIMER REMARK 220 AS FREQUENTLY NOTICED IN OTHER SYSTEMS. STEP THREE. REMARK 220 RECOGNITION OF HIGH SEQUENCE SIMILARITY OF THIS REMARK 220 CONSENSUS OPERATOR SEQUENCE WITH THAT OF THE LAMBDA REMARK 220 BACTERIOPHAGE CI REPRESSOR OPERATOR CONSENSUS SEQUENCE REMARK 220 (REF.12) WHEN CONSIDERED IN THE REVERSE DIRECTION : 5'- REMARK 220 GGTGGCTGTCAAG-3' L1/L5 CONSENSUS OPERATOR 3'- REMARK 220 CCACCGACAGTTC-5' 5'-TATCACCGCCAGTGGTA-3' LAMBDA CI REMARK 220 OPERATOR 17-BP 3'-ATAGTGGCGGTCACCAT-5' IN OTHER WORDS, REMARK 220 THE 3'-5' SEQUENCE OF L1/L5 MATCHES TO A LARGE EXTENT REMARK 220 THE 5'-3' SEQUENCE OF LAMBDA CI OPERATOR. THIS MEANS REMARK 220 THAT THOUGH THE 5'-3' SEQUENCES ARE DIFFERENT, BOTH REMARK 220 OPERATORS HAVE THE SAME BASE-PAIR AT 11 OF THE 12 COMMON REMARK 220 POSITIONS LEAVING OUT THE CENTRAL BASE PAIR. THIS MEANS, REMARK 220 THE DNA-BINDING OR STRUCTURES AS THEY EVENTUALLY HAVE TO REMARK 220 BIND SIMILAR MAJOR GROOVES. STEP FOUR. SUBMISSION OF THE REMARK 220 ENTIRE 183 AMINO ACID L1 REPRESSOR SEQUENCE FOR REMARK 220 SEARCHING STRUCTURAL TEMPLATES BY THE PROGRAM 3D-PSSM REMARK 220 (REF.11) WAS NOT VERY SUCCESSFUL. NO SIGNIFICANT REMARK 220 HOMOLOGS WERE DETECTED. HOWEVER, WHEN EITHER RESIDUES 1- REMARK 220 89 OR 1-110 WERE USED AS A QUERY SEQUENCE, ALL ALPHA REMARK 220 DOMAINS WERE DETECTED WITH MUCH LOWER E-VALUES OF 1.1 TO REMARK 220 9.5. AMONG THESE, THE REPRESSORS OF THE LAMBDOID PHAGES, REMARK 220 LIKE P22 C2 REPRESSOR (PDB CODE 1ADR) AND 434 REPRESSOR REMARK 220 (PDB CODE 1R69) WERE PRESENT, AS WELL AS CRO REPRESSOR REMARK 220 (PDB CODE 2CRO). THE E-VALUES FOR THESE IMPROVED REMARK 220 (REDUCED) WHEN RESIDUES 1-89 WERE USED INSTEAD OF 1-110. REMARK 220 STEP FIVE. WE KNOW THAT THE LAMBDOID PHAGE REPRESSORS REMARK 220 POSSESS DNA-BINDING N-DOMAINS WITH 70-92 RESIDUES. IT IS REMARK 220 LIKELY THAT L1/L5 PHAGE REPRESSOR POSSESSES LESS THAN 92 REMARK 220 RESIDUES IN ITS DNA-BINDING DOMAIN SINCE IT HAS A TOTAL REMARK 220 OF 183 RESIDUES, MUCH LESS COMPARED TO THE LAMBDA CI. REMARK 220 EVEN THE PHAGE REPRESSORS OF P22 AND 434 CONTAIN LESS REMARK 220 RESIDUES IN THEIR DNA BINDING N-DOMAINS. PARTICULARLY, REMARK 220 CI REPRESSOR HAS ABOUT 10-15 EXTRA RESIDUES AT THE N- REMARK 220 TERMINUS LACKING IN THESE OTHER LAMBDOID REPRESSORS. AS REMARK 220 THE THREE DIMENSIONAL STRUCTURES OF ALL THE LAMBDOID REMARK 220 REPRESSORS MENTIONED ARE HIGHLY SIMILAR, THE LAMBDA REMARK 220 REPRESSOR CI STRUCTURE WAS USED AS A TEMPLATE FOR L1/L5 REMARK 220 REPRESSOR TILL RESIDUE LYS 81 EVENTUALLY. FOLLOWING REMARK 220 CLUSTALW ALIGNMENT WAS USED : 1 28 L1 : ----------- REMARK 220 MSGKIQHKAVVPAPSRIPLTLSEIEDLR CI : REMARK 220 MSTKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVAD 1 39 29 66 L1 : REMARK 220 RKGFNQTEIAELYGVTRQAVSWHKKTYGGRLTT-RQIVQ CI : REMARK 220 KMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFS 40 78 81 L1 : REMARK 220 QNWPWDTRKPHDKSK CI : PSIAREIYEMYEAVS 79 93 NOTE THAT PDB REMARK 220 ENTRY 1LMB DOES NOT HAVE THE FIRST METHIONINE, SO SER 93 REMARK 220 ABOVE IS NAMED SER 92 IN 1LMB THE L1 N-DOMAIN DIMER WAS REMARK 220 PLACED ON THE DNA OPERATOR FOR THE CI REPRESSOR, THEN REMARK 220 THE APPROPRIATE BASES IN THAT OPERATOR WERE REPLACED REMARK 220 ACCORDING TO THE CONSENSUS SEQUENCE OF THE L1/L5 REMARK 220 OPERATOR. STEP SIX. BUILDING THE C-TERMINAL DOMAIN WAS REMARK 220 MORE COMPLEX, BUT IT BORROWED ELEMENTS FROM THE UMUD', REMARK 220 LAMBDA CI AND LEXA C-DOMAINS (REFS.4,5). THE 3D-PSSM REMARK 220 SEARCHES USING RESIDUES 110-183 WERE NOT SUCCESSFUL, NOR REMARK 220 RESIDUES 91-183. THE MOST IMPORTANT CLUE FOR THIS MODEL REMARK 220 BUILDING UTILIZES THE FACT THAT THE L1 REPRESSOR REMARK 220 AUTOCLEAVES ITSELF IN A PH-DEPENDENT FASHION (REFS.6,7) REMARK 220 LIKE LEXA, CI. HOWEVER L1/L5 POSSESS A REALLY REMARK 220 RUDIMENTARY C-DOMAIN COMPARED TO LEXA, CI. IN CASE OF REMARK 220 L1/L5 REPRESSORS, THERE EXISTS NO SUCH LYSINE IN THE C- REMARK 220 DOMAIN AS WITH LEXA OR CI REPRESSORS. HENCE IT IS REMARK 220 SUGGESTED A CATALYTIC SERINE 128 PLUS A CATALYTIC REMARK 220 HISTIDINE 159 TOGETHER CARRY OUT THE AUTOCLEAVAGE AT REMARK 220 ALA136-GLY137. THOUGH THE 3D-PSSM WAS NOT SUCCESSFUL REMARK 220 USING RESIDUES 91-183, SEARCH FOR A STRUCTURAL HOMOLOG REMARK 220 FOR A PART OF THE LINKER REGION WAS WHEN THE SEARCH WAS REMARK 220 CARRIED OUT USING RESIDUES 71-129. ACCORDINGLY, RESIDUES REMARK 220 82-116 HAVE BEEN MODELLED BASED ON THE CRYSTAL STRUCTURE REMARK 220 OF AN UNUSUAL PROCESSIVITY FACTOR, HSV UL42 BOUND TO THE REMARK 220 C-TERMINUS OF ITS COGNATE DNA POLYMERASE (REF.3). 82 116 REMARK 220 L1 : AFQRLRDHGEYMRVGSFRTMSEDKKRLLSWWKMLR 1DML VAARLRAAG- REMARK 220 FGAVGAGATAEETRRMLHRAFDTLA FURTHER DETAILS AND REMARK 220 BIOCHEMICAL DATA WILL BE PRESENTED IN OUR PUBLICATION. REMARK 220 REFINEMENT WAS CARRIED OUT USING THE INSIGHT-II PACKAGE REMARK 220 INCLUDING PROGRAMS DISCOVER 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 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 O1P A C 35 CG GLU A 36 1.59 REMARK 500 O1P A D 15 CG GLU B 36 1.63 REMARK 500 O1P A C 36 OD1 ASN A 33 2.10 REMARK 500 O1P A D 15 CD GLU B 36 2.18 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 ILE A 5 CB - CA - C ANGL. DEV. = 27.8 DEGREES REMARK 500 PRO A 12 CA - N - CD ANGL. DEV. =-25.0 DEGREES REMARK 500 PRO A 14 CA - N - CD ANGL. DEV. =-22.9 DEGREES REMARK 500 PHE A 32 N - CA - CB ANGL. DEV. =-25.6 DEGREES REMARK 500 PHE A 32 CA - CB - CG ANGL. DEV. = 36.4 DEGREES REMARK 500 ARG A 62 N - CA - CB ANGL. DEV. =-37.0 DEGREES REMARK 500 ARG A 62 CA - CB - CG ANGL. DEV. = 27.5 DEGREES REMARK 500 PRO A 70 CA - N - CD ANGL. DEV. =-22.5 DEGREES REMARK 500 PRO A 76 CA - N - CD ANGL. DEV. =-36.8 DEGREES REMARK 500 PRO A 76 N - CA - CB ANGL. DEV. = 25.5 DEGREES REMARK 500 PRO A 76 N - CD - CG ANGL. DEV. = 29.8 DEGREES REMARK 500 ILE B 5 CB - CA - C ANGL. DEV. = 27.8 DEGREES REMARK 500 PRO B 12 CA - N - CD ANGL. DEV. =-25.0 DEGREES REMARK 500 PRO B 14 CA - N - CD ANGL. DEV. =-22.9 DEGREES REMARK 500 PHE B 32 N - CA - CB ANGL. DEV. =-25.6 DEGREES REMARK 500 PHE B 32 CA - CB - CG ANGL. DEV. = 36.3 DEGREES REMARK 500 PRO B 70 CA - N - CD ANGL. DEV. =-22.4 DEGREES REMARK 500 PRO B 76 CA - N - CD ANGL. DEV. =-37.6 DEGREES REMARK 500 PRO B 76 N - CA - CB ANGL. DEV. = 24.3 DEGREES REMARK 500 PRO B 76 N - CD - CG ANGL. DEV. = 29.4 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 LYS A 81 -128.24 116.63 REMARK 500 GLU A 167 -64.06 70.88 REMARK 500 LYS B 81 -111.18 97.20 REMARK 500 ALA B 82 -101.06 -156.23 REMARK 500 GLU B 167 -64.13 70.94 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 LEU A 116 ARG A 117 147.39 REMARK 500 TYR A 142 VAL A 143 -144.64 REMARK 500 LEU B 116 ARG B 117 147.40 REMARK 500 TYR B 142 VAL B 143 -144.64

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MVD RELATED DB: PDB REMARK 900 RELATED ID: 1QAA RELATED DB: PDB REMARK 900 RELATED ID: 1LWQ RELATED DB: PDB REMARK 900 RELATED ID: 1J5G RELATED DB: PDB

DBREF 1Z0L A 1 183 UNP Q05286 VG71_BPML5 1 183 DBREF 1Z0L B 1 183 UNP Q05286 VG71_BPML5 1 183

SEQRES 1 A 183 MET SER GLY LYS ILE GLN HIS LYS ALA VAL VAL PRO ALA SEQRES 2 A 183 PRO SER ARG ILE PRO LEU THR LEU SER GLU ILE GLU ASP SEQRES 3 A 183 LEU ARG ARG LYS GLY PHE ASN GLN THR GLU ILE ALA GLU SEQRES 4 A 183 LEU TYR GLY VAL THR ARG GLN ALA VAL SER TRP HIS LYS SEQRES 5 A 183 LYS THR TYR GLY GLY ARG LEU THR THR ARG GLN ILE VAL SEQRES 6 A 183 GLN GLN ASN TRP PRO TRP ASP THR ARG LYS PRO HIS ASP SEQRES 7 A 183 LYS SER LYS ALA PHE GLN ARG LEU ARG ASP HIS GLY GLU SEQRES 8 A 183 TYR MET ARG VAL GLY SER PHE ARG THR MET SER GLU ASP SEQRES 9 A 183 LYS LYS LYS ARG LEU LEU SER TRP TRP LYS MET LEU ARG SEQRES 10 A 183 ASP ASP ASP LEU VAL LEU GLU PHE ASP PRO SER ILE GLU SEQRES 11 A 183 PRO TYR GLU GLY MET ALA GLY GLY GLY PHE ARG TYR VAL SEQRES 12 A 183 PRO ARG GLY ILE GLU ASP ASP ASP LEU LEU ILE ARG VAL SEQRES 13 A 183 ASN GLU HIS THR ASN LEU THR ALA GLU GLY GLU LEU LEU SEQRES 14 A 183 TRP SER TRP PRO ASP ASP ILE GLU GLU LEU LEU SER GLU SEQRES 15 A 183 PRO SEQRES 1 B 183 MET SER GLY LYS ILE GLN HIS LYS ALA VAL VAL PRO ALA SEQRES 2 B 183 PRO SER ARG ILE PRO LEU THR LEU SER GLU ILE GLU ASP SEQRES 3 B 183 LEU ARG ARG LYS GLY PHE ASN GLN THR GLU ILE ALA GLU SEQRES 4 B 183 LEU TYR GLY VAL THR ARG GLN ALA VAL SER TRP HIS LYS SEQRES 5 B 183 LYS THR TYR GLY GLY ARG LEU THR THR ARG GLN ILE VAL SEQRES 6 B 183 GLN GLN ASN TRP PRO TRP ASP THR ARG LYS PRO HIS ASP SEQRES 7 B 183 LYS SER LYS ALA PHE GLN ARG LEU ARG ASP HIS GLY GLU SEQRES 8 B 183 TYR MET ARG VAL GLY SER PHE ARG THR MET SER GLU ASP SEQRES 9 B 183 LYS LYS LYS ARG LEU LEU SER TRP TRP LYS MET LEU ARG SEQRES 10 B 183 ASP ASP ASP LEU VAL LEU GLU PHE ASP PRO SER ILE GLU SEQRES 11 B 183 PRO TYR GLU GLY MET ALA GLY GLY GLY PHE ARG TYR VAL SEQRES 12 B 183 PRO ARG GLY ILE GLU ASP ASP ASP LEU LEU ILE ARG VAL SEQRES 13 B 183 ASN GLU HIS THR ASN LEU THR ALA GLU GLY GLU LEU LEU SEQRES 14 B 183 TRP SER TRP PRO ASP ASP ILE GLU GLU LEU LEU SER GLU SEQRES 15 B 183 PRO SEQRES 1 C 20 T A T A G G T G G C T G T SEQRES 2 C 20 C A A G T A T SEQRES 1 D 20 A A T A C T T G A C A G C SEQRES 2 D 20 C A C C T A T

HELIX 1 1 MET A 1 VAL A 11 1 11 HELIX 2 2 VAL A 11 THR A 20 1 10 HELIX 3 3 SER A 22 GLY A 31 1 10 HELIX 4 4 ASN A 33 GLY A 42 1 10 HELIX 5 5 VAL A 48 THR A 60 1 13 HELIX 6 6 GLN A 67 ASP A 78 1 12 HELIX 7 7 GLN A 84 GLY A 90 1 7 HELIX 8 8 THR A 100 MET A 115 1 16 HELIX 9 9 MET B 1 VAL B 11 1 11 HELIX 10 10 VAL B 11 THR B 20 1 10 HELIX 11 11 SER B 22 GLY B 31 1 10 HELIX 12 12 ASN B 33 GLY B 42 1 10 HELIX 13 13 VAL B 48 THR B 60 1 13 HELIX 14 14 GLN B 67 ASP B 78 1 12 HELIX 15 15 ALA B 82 GLY B 90 1 9 HELIX 16 16 THR B 100 MET B 115 1 16

SHEET 1 A 8 ARG A 94 GLY A 96 0 SHEET 2 A 8 ASP A 120 GLU A 124 1 O VAL A 122 N VAL A 95 SHEET 3 A 8 GLY A 139 PRO A 144 -1 O ARG A 141 N LEU A 123 SHEET 4 A 8 GLU A 177 SER A 181 -1 O LEU A 179 N PHE A 140 SHEET 5 A 8 GLU B 177 SER B 181 -1 O GLU B 178 N LEU A 180 SHEET 6 A 8 GLY B 139 PRO B 144 -1 N PHE B 140 O LEU B 179 SHEET 7 A 8 ASP B 120 GLU B 124 -1 N LEU B 123 O ARG B 141 SHEET 8 A 8 ARG B 94 GLY B 96 1 N VAL B 95 O VAL B 122

CISPEP 1 GLU A 130 PRO A 131 0 5.65 CISPEP 2 GLU B 130 PRO B 131 0 5.67

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