HEADER UNKNOWN FUNCTION 04-FEB-03 1NVO TITLE SOLUTION STRUCTURE OF A FOUR-HELIX BUNDLE MODEL, APO-DF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMODIMERIC ALPHA2 FOUR-HELIX BUNDLE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DE NOVO PROTEIN DESIGN, ALPHA-HELICAL BUNDLE, DIIRON PROTEIN MODEL, KEYWDS 2 UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR O.MAGLIO,F.NASTRI,V.PAVONE,A.LOMBARDI,W.F.DEGRADO REVDAT 5 23-FEB-22 1NVO 1 REMARK LINK REVDAT 4 24-FEB-09 1NVO 1 VERSN REVDAT 3 13-JAN-04 1NVO 1 JRNL REVDAT 2 02-APR-03 1NVO 1 JRNL REVDAT 1 25-MAR-03 1NVO 0 JRNL AUTH O.MAGLIO,F.NASTRI,V.PAVONE,A.LOMBARDI,W.F.DEGRADO JRNL TITL PREORGANIZATION OF MOLECULAR BINDING SITES IN DESIGNED JRNL TITL 2 DIIRON PROTEINS JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 3772 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12655072 JRNL DOI 10.1073/PNAS.0730771100 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.LOMBARDI,C.M.SUMMA,S.GEREMIA,L.RANDACCIO,V.PAVONE, REMARK 1 AUTH 2 W.F.DEGRADO REMARK 1 TITL RETROSTRUCTURAL ANALYSIS OF METALLOPROTEINS. APPLICATION TO REMARK 1 TITL 2 THE DESIGN OF A MINIMAL MODEL FOR DIIRON PROTEINS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 97 6298 2000 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.97.12.6298 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.M.SUMMA,A.LOMBARDI,M.LEWIS,W.F.DEGRADO REMARK 1 TITL TERTIARY TEMPLATES FOR THE DESIGN OF DIIRON PROTEIN REMARK 1 REF CURR.OPIN.STRUCT.BIOL. V. 9 500 1999 REMARK 1 REFN ISSN 0959-440X REMARK 1 DOI 10.1016/S0959-440X(99)80071-2 REMARK 1 REFERENCE 3 REMARK 1 AUTH L.DI COSTANZO,H.WADE,S.GEREMIA,L.RANDACCIO,V.PAVONE, REMARK 1 AUTH 2 W.F.DEGRADO,A.LOMBARDI REMARK 1 TITL TOWARD THE DE NOVO DESIGN OF A CATALYTICALLY ACTIVE HELIX REMARK 1 TITL 2 BUNDLE: A SUBSTRATE-ACCESSIBLE CARBOXYLATE-BRIDGED DINUCLEAR REMARK 1 TITL 3 METAL CENTER REMARK 1 REF J.AM.CHEM.SOC. V. 123 12749 2001 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA010506X REMARK 1 REFERENCE 4 REMARK 1 AUTH W.F.DEGRADO,L.DI COSTANZO,S.GEREMIA,A.LOMBARDI,V.PAVONE, REMARK 1 AUTH 2 L.RANDACCIO REMARK 1 TITL SLIDING HELIX AND CHANGE OF COORDINATION GEOMETRY IN A MODEL REMARK 1 TITL 2 DI-MN(II) PROTEIN REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 42 417 2003 REMARK 1 REFN ESSN 0570-0833 REMARK 1 DOI 10.1002/ANIE.200390127 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, AMBER 7.0 REMARK 3 AUTHORS : DELAGLIO ET AL. (NMRPIPE), CASE ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NVO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018255. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM PROTEIN CONCENTRATION; REMARK 210 90% H2O, 10% DMSO REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D NOESY; 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 : DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, ENERGY REMARK 210 RESTRAINED MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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 TYR A 2 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 6 TYR A 2 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 TYR A 2 CB - CG - CD2 ANGL. DEV. = -3.8 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 LEU A 7 -43.46 -131.33 REMARK 500 1 GLU A 44 27.56 -75.92 REMARK 500 1 THR A 45 -51.01 -148.30 REMARK 500 1 LEU A 47 -54.14 72.53 REMARK 500 1 LEU B 7 -61.79 -145.59 REMARK 500 2 TYR A 2 -55.35 -19.10 REMARK 500 2 LEU A 6 37.51 -95.19 REMARK 500 2 LEU A 7 -57.83 -144.51 REMARK 500 2 ILE A 46 -58.31 -26.25 REMARK 500 2 LEU A 47 134.02 -170.71 REMARK 500 2 TYR B 2 -69.76 -26.81 REMARK 500 2 LEU B 7 -66.45 -151.39 REMARK 500 2 GLU B 44 35.75 -76.86 REMARK 500 2 THR B 45 -48.27 -150.22 REMARK 500 2 ILE B 46 66.22 36.21 REMARK 500 3 LEU A 7 -51.95 -130.99 REMARK 500 3 ILE A 46 67.55 35.67 REMARK 500 3 LEU A 47 16.20 57.87 REMARK 500 3 GLU B 5 -50.24 -137.44 REMARK 500 4 GLU A 5 -63.33 -102.59 REMARK 500 4 LEU A 6 33.97 -83.67 REMARK 500 4 LEU A 7 -55.47 -143.66 REMARK 500 4 GLU B 5 -74.07 -102.28 REMARK 500 4 LEU B 47 -138.47 64.63 REMARK 500 5 LEU A 7 -47.78 -135.67 REMARK 500 5 LYS A 25 63.99 61.69 REMARK 500 5 THR A 45 -46.43 -152.71 REMARK 500 5 LEU A 47 79.80 62.87 REMARK 500 5 LEU B 7 -62.66 -133.60 REMARK 500 5 GLU B 44 27.30 -75.47 REMARK 500 5 THR B 45 -45.46 -150.16 REMARK 500 5 ILE B 46 49.20 39.80 REMARK 500 6 LEU A 7 -58.09 -160.58 REMARK 500 6 GLU B 5 -69.46 -127.28 REMARK 500 6 LEU B 7 -53.77 -140.20 REMARK 500 6 LYS B 25 71.11 62.40 REMARK 500 6 ILE B 46 111.03 -27.28 REMARK 500 7 TYR A 2 -57.58 -20.01 REMARK 500 7 GLU A 5 -66.13 -98.23 REMARK 500 7 GLU B 5 -160.77 -112.65 REMARK 500 7 LEU B 7 -59.59 -177.62 REMARK 500 7 GLU B 44 36.94 -77.79 REMARK 500 7 THR B 45 -49.11 -156.65 REMARK 500 7 ILE B 46 -136.55 43.69 REMARK 500 8 LEU A 3 66.61 -164.12 REMARK 500 8 ARG A 4 -7.65 -153.89 REMARK 500 8 LEU A 7 -51.95 -129.18 REMARK 500 8 GLU B 5 -76.88 -125.73 REMARK 500 8 LEU B 6 6.78 -68.02 REMARK 500 8 LEU B 7 -56.31 -127.49 REMARK 500 REMARK 500 THIS ENTRY HAS 98 RAMACHANDRAN OUTLIERS. 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 1 TYR A 2 0.09 SIDE CHAIN REMARK 500 1 TYR B 2 0.07 SIDE CHAIN REMARK 500 1 TYR B 17 0.09 SIDE CHAIN REMARK 500 2 TYR B 2 0.10 SIDE CHAIN REMARK 500 3 TYR A 2 0.18 SIDE CHAIN REMARK 500 3 TYR A 17 0.09 SIDE CHAIN REMARK 500 3 TYR B 2 0.07 SIDE CHAIN REMARK 500 4 TYR A 2 0.08 SIDE CHAIN REMARK 500 4 TYR B 2 0.07 SIDE CHAIN REMARK 500 4 TYR B 17 0.09 SIDE CHAIN REMARK 500 5 TYR A 17 0.07 SIDE CHAIN REMARK 500 6 TYR B 2 0.08 SIDE CHAIN REMARK 500 7 TYR A 17 0.13 SIDE CHAIN REMARK 500 8 TYR B 2 0.09 SIDE CHAIN REMARK 500 9 TYR B 2 0.09 SIDE CHAIN REMARK 500 10 TYR A 2 0.07 SIDE CHAIN REMARK 500 10 TYR A 23 0.08 SIDE CHAIN REMARK 500 11 TYR A 17 0.09 SIDE CHAIN REMARK 500 12 TYR A 17 0.14 SIDE CHAIN REMARK 500 12 TYR B 2 0.14 SIDE CHAIN REMARK 500 13 TYR A 2 0.10 SIDE CHAIN REMARK 500 13 TYR A 17 0.07 SIDE CHAIN REMARK 500 13 ARG B 4 0.09 SIDE CHAIN REMARK 500 13 TYR B 17 0.07 SIDE CHAIN REMARK 500 14 TYR B 17 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 49 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 49 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EC5 RELATED DB: PDB REMARK 900 1EC5 IS THE CRYSTAL STRUCTURE OF DF1-DI-ZN(II) DERIVATIVE REMARK 900 RELATED ID: 1JMB RELATED DB: PDB REMARK 900 1JMB IS THE CRYSTAL STRUCTURE OF A DF1 MUTANT (L13A-DF1) IN THE DI- REMARK 900 MN(II) FORM (S.G. C 2 2 21) REMARK 900 RELATED ID: 1JM0 RELATED DB: PDB REMARK 900 1JM0 IS A DIFFERENT CRYSTALLINE FORM (S. G. P212121) OF 1JMB REMARK 900 RELATED ID: 1LT1 RELATED DB: PDB REMARK 900 1LT1 IS THE CRYSTAL STRUCTURE OF L13G-DF1 IN THE DI-MN(II) FORM DBREF 1NVO A 0 49 PDB 1NVO 1NVO 0 49 DBREF 1NVO B 0 49 PDB 1NVO 1NVO 0 49 SEQRES 1 A 50 ACE ASP TYR LEU ARG GLU LEU LEU LYS LEU GLU LEU GLN SEQRES 2 A 50 LEU ILE LYS GLN TYR ARG GLU ALA LEU GLU TYR VAL LYS SEQRES 3 A 50 LEU PRO VAL LEU ALA LYS ILE LEU GLU ASP GLU GLU LYS SEQRES 4 A 50 HIS ILE GLU TRP LEU GLU THR ILE LEU GLY NH2 SEQRES 1 B 50 ACE ASP TYR LEU ARG GLU LEU LEU LYS LEU GLU LEU GLN SEQRES 2 B 50 LEU ILE LYS GLN TYR ARG GLU ALA LEU GLU TYR VAL LYS SEQRES 3 B 50 LEU PRO VAL LEU ALA LYS ILE LEU GLU ASP GLU GLU LYS SEQRES 4 B 50 HIS ILE GLU TRP LEU GLU THR ILE LEU GLY NH2 HET ACE A 0 6 HET NH2 A 49 3 HET ACE B 0 6 HET NH2 B 49 3 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 NH2 2(H2 N) HELIX 1 1 LEU A 7 LYS A 25 1 19 HELIX 2 2 LEU A 26 GLU A 44 1 19 HELIX 3 3 ASP B 1 LEU B 7 1 7 HELIX 4 4 LEU B 7 TYR B 23 1 17 HELIX 5 5 LEU B 26 ILE B 46 1 21 LINK C ACE A 0 N ASP A 1 1555 1555 1.34 LINK C GLY A 48 N NH2 A 49 1555 1555 1.33 LINK C ACE B 0 N ASP B 1 1555 1555 1.34 LINK C GLY B 48 N NH2 B 49 1555 1555 1.33 SITE 1 AC3 1 GLY A 48 SITE 1 AC4 1 GLY B 48 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 MODEL 1 HETATM 1 C ACE A 0 1.621 7.627 7.194 1.00 0.00 C HETATM 2 O ACE A 0 1.078 7.112 8.166 1.00 0.00 O HETATM 3 CH3 ACE A 0 2.958 7.096 6.697 1.00 0.00 C HETATM 4 H1 ACE A 0 3.715 7.875 6.778 1.00 0.00 H HETATM 5 H2 ACE A 0 2.862 6.784 5.657 1.00 0.00 H HETATM 6 H3 ACE A 0 3.260 6.238 7.299 1.00 0.00 H