PDB Short entry for 5KVI HEADER OXIDOREDUCTASE 14-JUL-16 5KVI TITLE CRYSTAL STRUCTURE OF MONOMERIC HUMAN APOPTOSIS-INDUCING FACTOR WITH TITLE 2 E413A/R422A/R430A MUTATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROGRAMMED CELL DEATH PROTEIN 8; COMPND 5 EC: 1.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: EXPRESSED AS AIF(78-613). RESIDUES L614-Q619 REMAIN COMPND 9 FROM PRESCISSION PROTEASE CLEAVAGE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AIFM1, AIF, PDCD8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24B KEYWDS OXIDOREDUCTASE, FLAVOPROTEIN, MITOCHONDRIA CELL DEATH EXPDTA X-RAY DIFFRACTION AUTHOR C.A.BROSEY,J.NIX,T.ELLENBERGER,J.A.TAINER REVDAT 5 04-OCT-23 5KVI 1 REMARK REVDAT 4 04-DEC-19 5KVI 1 REMARK REVDAT 3 06-SEP-17 5KVI 1 REMARK REVDAT 2 14-DEC-16 5KVI 1 JRNL REVDAT 1 16-NOV-16 5KVI 0 JRNL AUTH C.A.BROSEY,C.HO,W.Z.LONG,S.SINGH,K.BURNETT,G.L.HURA,J.C.NIX, JRNL AUTH 2 G.R.BOWMAN,T.ELLENBERGER,J.A.TAINER JRNL TITL DEFINING NADH-DRIVEN ALLOSTERY REGULATING APOPTOSIS-INDUCING JRNL TITL 2 FACTOR. JRNL REF STRUCTURE V. 24 2067 2016 JRNL REFN ISSN 1878-4186 JRNL PMID 27818101 JRNL DOI 10.1016/J.STR.2016.09.012 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.2 REMARK 3 NUMBER OF REFLECTIONS : 31943 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1590 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.1715 - 4.4352 0.99 3621 211 0.1510 0.1716 REMARK 3 2 4.4352 - 3.5208 1.00 3459 195 0.1323 0.1711 REMARK 3 3 3.5208 - 3.0758 1.00 3460 162 0.1513 0.1950 REMARK 3 4 3.0758 - 2.7947 1.00 3435 194 0.1733 0.2553 REMARK 3 5 2.7947 - 2.5944 1.00 3418 175 0.1836 0.2243 REMARK 3 6 2.5944 - 2.4414 0.94 3238 150 0.1836 0.2080 REMARK 3 7 2.4414 - 2.3192 0.83 2806 150 0.1656 0.2191 REMARK 3 8 2.3192 - 2.2182 0.70 2357 129 0.1577 0.2063 REMARK 3 9 2.2182 - 2.1328 0.56 1909 97 0.1628 0.1723 REMARK 3 10 2.1328 - 2.0592 0.45 1513 80 0.1746 0.2233 REMARK 3 11 2.0592 - 1.9948 0.33 1137 47 0.2106 0.2193 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.37 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3815 REMARK 3 ANGLE : 0.876 5169 REMARK 3 CHIRALITY : 0.053 571 REMARK 3 PLANARITY : 0.005 660 REMARK 3 DIHEDRAL : 11.514 2257 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 129 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): -40.0107 87.4884 -0.5301 REMARK 3 T TENSOR REMARK 3 T11: 0.3808 T22: 0.2271 REMARK 3 T33: 0.1612 T12: -0.0654 REMARK 3 T13: -0.0500 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.4649 L22: 1.2434 REMARK 3 L33: 1.9843 L12: 0.1459 REMARK 3 L13: 0.4191 L23: 0.1819 REMARK 3 S TENSOR REMARK 3 S11: -0.0472 S12: 0.2788 S13: -0.1128 REMARK 3 S21: -0.5348 S22: 0.0682 S23: 0.0993 REMARK 3 S31: -0.0072 S32: 0.0449 S33: -0.0241 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 246 THROUGH 402 ) REMARK 3 ORIGIN FOR THE GROUP (A): -53.9155 97.0826 19.7668 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.2514 REMARK 3 T33: 0.2810 T12: -0.0195 REMARK 3 T13: -0.0170 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 1.5079 L22: 1.5063 REMARK 3 L33: 1.7953 L12: -0.3019 REMARK 3 L13: -0.0729 L23: 0.7069 REMARK 3 S TENSOR REMARK 3 S11: -0.0320 S12: -0.0893 S13: 0.0149 REMARK 3 S21: -0.0205 S22: -0.0836 S23: 0.5254 REMARK 3 S31: -0.0419 S32: -0.4438 S33: 0.1253 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 403 THROUGH 611 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.6907 99.8851 17.9235 REMARK 3 T TENSOR REMARK 3 T11: 0.1679 T22: 0.1732 REMARK 3 T33: 0.1315 T12: -0.0552 REMARK 3 T13: 0.0117 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.8102 L22: 2.3252 REMARK 3 L33: 1.2939 L12: 0.1922 REMARK 3 L13: 0.2500 L23: 0.3606 REMARK 3 S TENSOR REMARK 3 S11: -0.0955 S12: 0.0016 S13: 0.0624 REMARK 3 S21: -0.2430 S22: 0.1981 S23: -0.2468 REMARK 3 S31: -0.2150 S32: 0.2327 S33: -0.0534 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS WERE INCLUDED IN RIDING REMARK 3 POSITIONS DURING REFINEMENT. FAD COFACTOR, HEPES, AND GLYCEROL REMARK 3 GEOMETRY RESTRAINTS WERE PREPARED IN ELBOW USING MOGUL (FAD) OR REMARK 3 SIMPLE OPTIMIZATION (HEPES, GLYCEROL) AND INCLUDED EXPLICITLY REMARK 3 WITH THE REFINEMENT. RESIDUES 78-125, 511-559, AND 613-619 ARE REMARK 3 DISORDERED IN CHAINS A AND B. REMARK 4 REMARK 4 5KVI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32041 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 31.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.0 REMARK 200 STARTING MODEL: 4BV6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7.5, 50 MM NACL, 24% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 32.31150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.16150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.90100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.16150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.31150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.90100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 2230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 77 REMARK 465 VAL A 78 REMARK 465 GLY A 79 REMARK 465 ALA A 80 REMARK 465 GLY A 81 REMARK 465 ALA A 82 REMARK 465 TYR A 83 REMARK 465 ALA A 84 REMARK 465 TYR A 85 REMARK 465 LYS A 86 REMARK 465 THR A 87 REMARK 465 MET A 88 REMARK 465 LYS A 89 REMARK 465 GLU A 90 REMARK 465 ASP A 91 REMARK 465 GLU A 92 REMARK 465 LYS A 93 REMARK 465 ARG A 94 REMARK 465 TYR A 95 REMARK 465 ASN A 96 REMARK 465 GLU A 97 REMARK 465 ARG A 98 REMARK 465 ILE A 99 REMARK 465 SER A 100 REMARK 465 GLY A 101 REMARK 465 LEU A 102 REMARK 465 GLY A 103 REMARK 465 LEU A 104 REMARK 465 THR A 105 REMARK 465 PRO A 106 REMARK 465 GLU A 107 REMARK 465 GLN A 108 REMARK 465 LYS A 109 REMARK 465 GLN A 110 REMARK 465 LYS A 111 REMARK 465 LYS A 112 REMARK 465 ALA A 113 REMARK 465 ALA A 114 REMARK 465 LEU A 115 REMARK 465 SER A 116 REMARK 465 ALA A 117 REMARK 465 SER A 118 REMARK 465 GLU A 119 REMARK 465 GLY A 120 REMARK 465 GLU A 121 REMARK 465 GLU A 122 REMARK 465 VAL A 123 REMARK 465 PRO A 124 REMARK 465 GLN A 125 REMARK 465 ASP A 126 REMARK 465 LYS A 127 REMARK 465 ALA A 128 REMARK 465 PRO A 545 REMARK 465 SER A 546 REMARK 465 THR A 547 REMARK 465 PRO A 548 REMARK 465 ALA A 549 REMARK 465 VAL A 550 REMARK 465 PRO A 551 REMARK 465 GLN A 552 REMARK 465 ALA A 553 REMARK 465 PRO A 554 REMARK 465 VAL A 555 REMARK 465 GLN A 556 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 ASP A 183 CG OD1 OD2 REMARK 470 LYS A 194 CD CE NZ REMARK 470 GLN A 215 CG CD OE1 NE2 REMARK 470 LYS A 388 CE NZ REMARK 470 LYS A 571 CD CE NZ REMARK 470 LYS A 593 CE NZ REMARK 470 LEU A 617 CB CG CD1 CD2 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 HE21 GLN A 619 O HOH A 805 1.58 REMARK 500 O HOH A 862 O HOH A 1128 1.68 REMARK 500 O HOH A 1114 O HOH A 1179 1.77 REMARK 500 O HOH A 1181 O HOH A 1247 1.92 REMARK 500 O HOH A 855 O HOH A 1200 1.94 REMARK 500 O HOH A 969 O HOH A 1174 1.96 REMARK 500 O HOH A 1142 O HOH A 1144 1.98 REMARK 500 O HOH A 941 O HOH A 950 2.06 REMARK 500 OD1 ASP A 485 NH1 ARG A 529 2.07 REMARK 500 O HOH A 1017 O HOH A 1221 2.09 REMARK 500 O HOH A 1199 O HOH A 1204 2.10 REMARK 500 O HOH A 859 O HOH A 861 2.16 REMARK 500 O HOH A 966 O HOH A 1195 2.19 REMARK 500 O HOH A 1150 O HOH A 1204 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 864 O HOH A 1139 3445 2.09 REMARK 500 O HOH A 1135 O HOH A 1177 4475 2.13 REMARK 500 O HOH A 872 O HOH A 899 4575 2.18 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 A 529 NE - CZ - NH1 ANGL. DEV. = -3.1 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 LYS A 177 -101.38 -133.58 REMARK 500 PHE A 181 53.63 -99.64 REMARK 500 ASP A 183 14.14 57.43 REMARK 500 LEU A 191 29.74 49.07 REMARK 500 ARG A 285 -36.36 -140.89 REMARK 500 GLU A 453 68.79 -118.56 REMARK 500 THR A 534 161.24 67.86 REMARK 500 ASP A 559 -152.09 -152.05 REMARK 500 ASP A 600 59.04 38.16 REMARK 500 ILE A 610 -62.27 -120.90 REMARK 500 ASP A 613 47.93 -91.53 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 598 GLU A 599 147.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1255 DISTANCE = 6.39 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 703 DBREF 5KVI A 78 613 UNP O95831 AIFM1_HUMAN 78 613 SEQADV 5KVI MET A 77 UNP O95831 INITIATING METHIONINE SEQADV 5KVI ALA A 413 UNP O95831 GLU 413 ENGINEERED MUTATION SEQADV 5KVI ALA A 422 UNP O95831 ARG 422 ENGINEERED MUTATION SEQADV 5KVI ALA A 430 UNP O95831 ARG 430 ENGINEERED MUTATION SEQADV 5KVI LEU A 614 UNP O95831 EXPRESSION TAG SEQADV 5KVI GLU A 615 UNP O95831 EXPRESSION TAG SEQADV 5KVI VAL A 616 UNP O95831 EXPRESSION TAG SEQADV 5KVI LEU A 617 UNP O95831 EXPRESSION TAG SEQADV 5KVI PHE A 618 UNP O95831 EXPRESSION TAG SEQADV 5KVI GLN A 619 UNP O95831 EXPRESSION TAG SEQRES 1 A 543 MET VAL GLY ALA GLY ALA TYR ALA TYR LYS THR MET LYS SEQRES 2 A 543 GLU ASP GLU LYS ARG TYR ASN GLU ARG ILE SER GLY LEU SEQRES 3 A 543 GLY LEU THR PRO GLU GLN LYS GLN LYS LYS ALA ALA LEU SEQRES 4 A 543 SER ALA SER GLU GLY GLU GLU VAL PRO GLN ASP LYS ALA SEQRES 5 A 543 PRO SER HIS VAL PRO PHE LEU LEU ILE GLY GLY GLY THR SEQRES 6 A 543 ALA ALA PHE ALA ALA ALA ARG SER ILE ARG ALA ARG ASP SEQRES 7 A 543 PRO GLY ALA ARG VAL LEU ILE VAL SER GLU ASP PRO GLU SEQRES 8 A 543 LEU PRO TYR MET ARG PRO PRO LEU SER LYS GLU LEU TRP SEQRES 9 A 543 PHE SER ASP ASP PRO ASN VAL THR LYS THR LEU ARG PHE SEQRES 10 A 543 LYS GLN TRP ASN GLY LYS GLU ARG SER ILE TYR PHE GLN SEQRES 11 A 543 PRO PRO SER PHE TYR VAL SER ALA GLN ASP LEU PRO HIS SEQRES 12 A 543 ILE GLU ASN GLY GLY VAL ALA VAL LEU THR GLY LYS LYS SEQRES 13 A 543 VAL VAL GLN LEU ASP VAL ARG ASP ASN MET VAL LYS LEU SEQRES 14 A 543 ASN ASP GLY SER GLN ILE THR TYR GLU LYS CYS LEU ILE SEQRES 15 A 543 ALA THR GLY GLY THR PRO ARG SER LEU SER ALA ILE ASP SEQRES 16 A 543 ARG ALA GLY ALA GLU VAL LYS SER ARG THR THR LEU PHE SEQRES 17 A 543 ARG LYS ILE GLY ASP PHE ARG SER LEU GLU LYS ILE SER SEQRES 18 A 543 ARG GLU VAL LYS SER ILE THR ILE ILE GLY GLY GLY PHE SEQRES 19 A 543 LEU GLY SER GLU LEU ALA CYS ALA LEU GLY ARG LYS ALA SEQRES 20 A 543 ARG ALA LEU GLY THR GLU VAL ILE GLN LEU PHE PRO GLU SEQRES 21 A 543 LYS GLY ASN MET GLY LYS ILE LEU PRO GLU TYR LEU SER SEQRES 22 A 543 ASN TRP THR MET GLU LYS VAL ARG ARG GLU GLY VAL LYS SEQRES 23 A 543 VAL MET PRO ASN ALA ILE VAL GLN SER VAL GLY VAL SER SEQRES 24 A 543 SER GLY LYS LEU LEU ILE LYS LEU LYS ASP GLY ARG LYS SEQRES 25 A 543 VAL GLU THR ASP HIS ILE VAL ALA ALA VAL GLY LEU GLU SEQRES 26 A 543 PRO ASN VAL GLU LEU ALA LYS THR GLY GLY LEU ALA ILE SEQRES 27 A 543 ASP SER ASP PHE GLY GLY PHE ALA VAL ASN ALA GLU LEU SEQRES 28 A 543 GLN ALA ALA SER ASN ILE TRP VAL ALA GLY ASP ALA ALA SEQRES 29 A 543 CYS PHE TYR ASP ILE LYS LEU GLY ARG ARG ARG VAL GLU SEQRES 30 A 543 HIS HIS ASP HIS ALA VAL VAL SER GLY ARG LEU ALA GLY SEQRES 31 A 543 GLU ASN MET THR GLY ALA ALA LYS PRO TYR TRP HIS GLN SEQRES 32 A 543 SER MET PHE TRP SER ASP LEU GLY PRO ASP VAL GLY TYR SEQRES 33 A 543 GLU ALA ILE GLY LEU VAL ASP SER SER LEU PRO THR VAL SEQRES 34 A 543 GLY VAL PHE ALA LYS ALA THR ALA GLN ASP ASN PRO LYS SEQRES 35 A 543 SER ALA THR GLU GLN SER GLY THR GLY ILE ARG SER GLU SEQRES 36 A 543 SER GLU THR GLU SER GLU ALA SER GLU ILE THR ILE PRO SEQRES 37 A 543 PRO SER THR PRO ALA VAL PRO GLN ALA PRO VAL GLN GLY SEQRES 38 A 543 GLU ASP TYR GLY LYS GLY VAL ILE PHE TYR LEU ARG ASP SEQRES 39 A 543 LYS VAL VAL VAL GLY ILE VAL LEU TRP ASN ILE PHE ASN SEQRES 40 A 543 ARG MET PRO ILE ALA ARG LYS ILE ILE LYS ASP GLY GLU SEQRES 41 A 543 GLN HIS GLU ASP LEU ASN GLU VAL ALA LYS LEU PHE ASN SEQRES 42 A 543 ILE HIS GLU ASP LEU GLU VAL LEU PHE GLN HET FAD A 701 84 HET EPE A 702 32 HET GOL A 703 14 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM GOL GLYCEROL HETSYN EPE HEPES HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *455(H2 O) HELIX 1 AA1 GLY A 140 ASP A 154 1 15 HELIX 2 AA2 ARG A 172 PHE A 181 5 10 HELIX 3 AA3 ASN A 186 LEU A 191 1 6 HELIX 4 AA4 PRO A 207 TYR A 211 5 5 HELIX 5 AA5 LEU A 267 ALA A 273 1 7 HELIX 6 AA6 GLY A 274 ARG A 280 1 7 HELIX 7 AA7 LYS A 286 VAL A 300 1 15 HELIX 8 AA8 GLY A 309 GLY A 327 1 19 HELIX 9 AA9 PRO A 345 GLU A 359 1 15 HELIX 10 AB1 VAL A 404 GLY A 410 5 7 HELIX 11 AB2 HIS A 454 MET A 469 1 16 HELIX 12 AB3 ASN A 516 GLY A 525 1 10 HELIX 13 AB4 ILE A 528 THR A 534 1 7 HELIX 14 AB5 ARG A 584 GLY A 595 1 12 HELIX 15 AB6 ASP A 600 ALA A 605 1 6 HELIX 16 AB7 ALA A 605 ILE A 610 1 6 SHEET 1 AA1 6 GLY A 224 THR A 229 0 SHEET 2 AA1 6 ARG A 158 SER A 163 1 N ILE A 161 O LEU A 228 SHEET 3 AA1 6 HIS A 131 ILE A 137 1 N LEU A 136 O LEU A 160 SHEET 4 AA1 6 GLN A 250 ILE A 258 1 O LEU A 257 N ILE A 137 SHEET 5 AA1 6 MET A 242 LEU A 245 -1 N VAL A 243 O ILE A 251 SHEET 6 AA1 6 VAL A 233 ASP A 237 -1 N ASP A 237 O MET A 242 SHEET 1 AA2 6 GLY A 224 THR A 229 0 SHEET 2 AA2 6 ARG A 158 SER A 163 1 N ILE A 161 O LEU A 228 SHEET 3 AA2 6 HIS A 131 ILE A 137 1 N LEU A 136 O LEU A 160 SHEET 4 AA2 6 GLN A 250 ILE A 258 1 O LEU A 257 N ILE A 137 SHEET 5 AA2 6 ILE A 433 VAL A 435 1 O TRP A 434 N ILE A 258 SHEET 6 AA2 6 GLN A 428 ALA A 430 -1 N ALA A 429 O ILE A 433 SHEET 1 AA3 2 ARG A 192 LYS A 194 0 SHEET 2 AA3 2 GLU A 200 SER A 202 -1 O ARG A 201 N PHE A 193 SHEET 1 AA4 2 GLY A 262 PRO A 264 0 SHEET 2 AA4 2 LEU A 400 PRO A 402 -1 O GLU A 401 N THR A 263 SHEET 1 AA5 5 THR A 281 LEU A 283 0 SHEET 2 AA5 5 HIS A 393 ALA A 396 1 O ILE A 394 N THR A 282 SHEET 3 AA5 5 SER A 302 ILE A 306 1 N ILE A 306 O VAL A 395 SHEET 4 AA5 5 GLU A 329 LEU A 333 1 O ILE A 331 N ILE A 305 SHEET 5 AA5 5 LYS A 362 MET A 364 1 O MET A 364 N GLN A 332 SHEET 1 AA6 3 VAL A 369 SER A 375 0 SHEET 2 AA6 3 LYS A 378 LEU A 383 -1 O LEU A 380 N GLY A 373 SHEET 3 AA6 3 LYS A 388 THR A 391 -1 O VAL A 389 N ILE A 381 SHEET 1 AA7 3 PHE A 421 ALA A 422 0 SHEET 2 AA7 3 ALA A 440 ASP A 444 1 O CYS A 441 N PHE A 421 SHEET 3 AA7 3 GLY A 448 ARG A 450 -1 O GLY A 448 N ASP A 444 SHEET 1 AA8 5 MET A 481 ASP A 485 0 SHEET 2 AA8 5 GLY A 491 GLY A 496 -1 O TYR A 492 N SER A 484 SHEET 3 AA8 5 VAL A 572 TRP A 579 -1 O LEU A 578 N GLU A 493 SHEET 4 AA8 5 LYS A 562 ARG A 569 -1 N TYR A 567 O GLY A 575 SHEET 5 AA8 5 THR A 504 ALA A 509 -1 N VAL A 505 O PHE A 566 SHEET 1 AA9 2 ALA A 538 THR A 542 0 SHEET 2 AA9 2 GLU A 615 PHE A 618 -1 O LEU A 617 N SER A 539 SITE 1 AC1 39 GLY A 138 GLY A 139 GLY A 140 THR A 141 SITE 2 AC1 39 ALA A 142 VAL A 162 GLU A 164 ASP A 165 SITE 3 AC1 39 ARG A 172 PRO A 173 SER A 176 LYS A 177 SITE 4 AC1 39 LYS A 232 VAL A 233 ALA A 259 THR A 260 SITE 5 AC1 39 GLY A 261 ARG A 285 LYS A 286 LEU A 311 SITE 6 AC1 39 GLY A 437 ASP A 438 GLU A 453 HIS A 454 SITE 7 AC1 39 HIS A 455 ALA A 458 PHE A 482 TRP A 483 SITE 8 AC1 39 HOH A 823 HOH A 830 HOH A 840 HOH A 843 SITE 9 AC1 39 HOH A 848 HOH A 857 HOH A 866 HOH A 883 SITE 10 AC1 39 HOH A 964 HOH A1007 HOH A1009 SITE 1 AC2 10 ARG A 265 LYS A 342 ILE A 343 VAL A 398 SITE 2 AC2 10 GLY A 399 HIS A 454 PHE A 482 HOH A 942 SITE 3 AC2 10 HOH A1050 HOH A1091 SITE 1 AC3 7 VAL A 423 ASN A 424 ARG A 449 HOH A 804 SITE 2 AC3 7 HOH A 807 HOH A1150 HOH A1197 CRYST1 64.623 81.802 108.323 90.00 90.00 90.00 P 21 21 21 4 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 0.015474 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012225 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009232 0.00000