HEADER DE NOVO PROTEIN 05-JUL-04 1VL3 TITLE DESIGN OF NEW MIMOCHROMES WITH UNIQUE TOPOLOGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLU-SER-GLN-LEU-HIS-SER-ASN-LYS-ARG; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS ALPHA-HELIX, DESIGN, MINIATURIZED METALLOPROTEINS, DE NOVO PROTEIN EXPDTA SOLUTION NMR AUTHOR A.LOMBARDI,F.NASTRI,D.MARASCO,O.MAGLIO,G.DE SANCTIS,F.SINIBALDI, AUTHOR 2 R.SANTUCCI,M.COLETTA,V.PAVONE REVDAT 3 31-AUG-11 1VL3 1 HETATM VERSN REVDAT 2 24-FEB-09 1VL3 1 VERSN REVDAT 1 20-JUL-04 1VL3 0 SPRSDE 20-JUL-04 1VL3 1L1B JRNL AUTH A.LOMBARDI,F.NASTRI,D.MARASCO,O.MAGLIO,G.DE SANCTIS, JRNL AUTH 2 F.SINIBALDI,R.SANTUCCI,M.COLETTA,V.PAVONE JRNL TITL DESIGN OF A NEW MIMOCHROME WITH UNIQUE TOPOLOGY. JRNL REF CHEMISTRY V. 9 5643 2003 JRNL REFN ISSN 0947-6539 JRNL PMID 14639648 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 250 NOE-DERIVED DISTANCE RESTRAINTS REMARK 4 REMARK 4 1VL3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-04. REMARK 100 THE RCSB ID CODE IS RCSB001969. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM CO(III)-MIMOCHROME IV 70% REMARK 210 H2O, 30% CF3CD2OD REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, DISCOVER REMARK 210 METHOD USED : MOLECULAR DYNAMIC SIMULATION FOR REMARK 210 400 PS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 DISTANCE REMARK 500 HH12 ARG A 9 OE2 GLU B 1 1.54 REMARK 500 HH22 ARG A 9 OE1 GLU B 1 1.55 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 ARG A 9 CZ ARG A 9 NH1 0.095 REMARK 500 ARG A 9 CZ ARG A 9 NH2 0.094 REMARK 500 ARG B 9 CZ ARG B 9 NH1 0.095 REMARK 500 ARG B 9 CZ ARG B 9 NH2 0.092 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 9 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 9 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 2 -64.68 -25.72 REMARK 500 LYS A 8 -69.04 61.99 REMARK 500 SER B 2 -53.81 -25.46 REMARK 500 SER B 6 -23.92 -38.70 REMARK 500 LYS B 8 -48.90 13.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DEU B 19 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 DEU B 19 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 5 NE2 REMARK 620 2 DEU B 19 NA 93.0 REMARK 620 3 DEU B 19 NB 89.6 89.7 REMARK 620 4 DEU B 19 NC 89.2 177.7 89.8 REMARK 620 5 DEU B 19 ND 89.4 90.7 179.0 89.8 REMARK 620 6 HIS B 5 NE2 178.0 88.3 88.9 89.5 92.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DEU B 19 DBREF 1VL3 A 0 10 PDB 1VL3 1VL3 0 10 DBREF 1VL3 B 0 10 PDB 1VL3 1VL3 0 10 SEQRES 1 A 11 ACE GLU SER GLN LEU HIS SER ASN LYS ARG NH2 SEQRES 1 B 11 ACE GLU SER GLN LEU HIS SER ASN LYS ARG NH2 HET ACE A 0 6 HET NH2 A 10 3 HET ACE B 0 6 HET NH2 B 10 3 HET DEU B 19 61 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM DEU CO(III)-(DEUTEROPORPHYRIN IX) FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 NH2 2(H2 N) FORMUL 3 DEU C30 H28 CO N4 O4 5+ HELIX 1 1 GLU A 1 LYS A 8 1 8 HELIX 2 2 GLU B 1 SER B 6 1 6 LINK NZ LYS A 8 CGA DEU B 19 1555 1555 1.35 LINK NZ LYS B 8 CGD DEU B 19 1555 1555 1.33 LINK NE2 HIS A 5 CO DEU B 19 1555 1555 2.05 LINK NE2 HIS B 5 CO DEU B 19 1555 1555 2.04 LINK C ACE A 0 N GLU A 1 1555 1555 1.33 LINK C ARG A 9 N NH2 A 10 1555 1555 1.33 LINK C ACE B 0 N GLU B 1 1555 1555 1.32 LINK C ARG B 9 N NH2 B 10 1555 1555 1.33 SITE 1 AC1 8 GLU A 1 HIS A 5 ASN A 7 LYS A 8 SITE 2 AC1 8 ARG A 9 GLU B 1 HIS B 5 LYS B 8 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 MASTER 169 0 5 2 0 0 2 6 0 0 0 2 END