HEADER IMMUNE SYSTEM 16-JAN-21 7LFB TITLE FAB 7D6 BOUND TO APOL1 NTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB 7D6 HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB 7D6 LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: APOLIPOPROTEIN L1; COMPND 11 CHAIN: X; COMPND 12 FRAGMENT: RESIDUES 61-172; COMPND 13 SYNONYM: APOLIPOPROTEIN L,APOL,APOLIPOPROTEIN L-I,APOL-I; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: 64B4; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: AEP1; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: 64B4; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: AEP1; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 GENE: APOL1, APOL; SOURCE 22 EXPRESSION_SYSTEM: BACULOVIRIDAE SP.; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 2681587 KEYWDS COMPLEX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.ULTSCH,D.KIRCHHOFER REVDAT 3 18-OCT-23 7LFB 1 REMARK REVDAT 2 16-FEB-22 7LFB 1 JRNL REVDAT 1 04-AUG-21 7LFB 0 JRNL AUTH M.ULTSCH,M.J.HOLLIDAY,S.GERHARDY,P.MORAN,S.J.SCALES,N.GUPTA, JRNL AUTH 2 F.OLTRABELLA,C.CHIU,W.FAIRBROTHER,C.EIGENBROT,D.KIRCHHOFER JRNL TITL STRUCTURES OF THE APOL1 AND APOL2 N-TERMINAL DOMAINS REVEAL JRNL TITL 2 A NON-CLASSICAL FOUR-HELIX BUNDLE MOTIF. JRNL REF COMMUN BIOL V. 4 916 2021 JRNL REFN ESSN 2399-3642 JRNL PMID 34316015 JRNL DOI 10.1038/S42003-021-02387-5 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 49456 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2504 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 49.6280 - 5.0116 0.97 2664 138 0.1540 0.1658 REMARK 3 2 5.0116 - 3.9784 0.94 2525 133 0.1316 0.1225 REMARK 3 3 3.9784 - 3.4756 0.95 2533 125 0.1556 0.2031 REMARK 3 4 3.4756 - 3.1579 0.96 2534 148 0.1625 0.2109 REMARK 3 5 3.1579 - 2.9316 0.98 2585 133 0.1765 0.1976 REMARK 3 6 2.9316 - 2.7588 0.99 2614 145 0.1725 0.2056 REMARK 3 7 2.7588 - 2.6206 0.99 2632 128 0.1795 0.2417 REMARK 3 8 2.6206 - 2.5065 0.99 2648 118 0.1787 0.2317 REMARK 3 9 2.5065 - 2.4101 1.00 2618 138 0.1801 0.1940 REMARK 3 10 2.4101 - 2.3269 1.00 2641 123 0.1783 0.2354 REMARK 3 11 2.3269 - 2.2541 0.99 2615 147 0.1800 0.2316 REMARK 3 12 2.2541 - 2.1897 1.00 2660 135 0.1866 0.2008 REMARK 3 13 2.1897 - 2.1321 1.00 2593 151 0.1837 0.2325 REMARK 3 14 2.1321 - 2.0800 1.00 2602 162 0.1882 0.2470 REMARK 3 15 2.0800 - 2.0328 1.00 2640 155 0.1950 0.2433 REMARK 3 16 2.0328 - 1.9895 1.00 2612 140 0.2107 0.2229 REMARK 3 17 1.9895 - 1.9497 1.00 2612 139 0.2300 0.2680 REMARK 3 18 1.9497 - 1.9130 1.00 2624 146 0.2708 0.3256 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.01 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 : 0.006 4161 REMARK 3 ANGLE : 0.961 5643 REMARK 3 CHIRALITY : 0.038 621 REMARK 3 PLANARITY : 0.004 725 REMARK 3 DIHEDRAL : 14.316 1514 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'H' AND RESID 1 THROUGH 224) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9392 -1.1379 45.0917 REMARK 3 T TENSOR REMARK 3 T11: 0.1698 T22: 0.2496 REMARK 3 T33: 0.3136 T12: -0.0138 REMARK 3 T13: 0.0179 T23: -0.0403 REMARK 3 L TENSOR REMARK 3 L11: 0.9094 L22: 1.0938 REMARK 3 L33: 1.4427 L12: 0.0750 REMARK 3 L13: 0.1233 L23: 0.0241 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: 0.1689 S13: -0.0234 REMARK 3 S21: -0.1079 S22: 0.0010 S23: -0.3138 REMARK 3 S31: -0.1491 S32: 0.4088 S33: -0.0030 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'L' AND RESID 1 THROUGH 214) REMARK 3 ORIGIN FOR THE GROUP (A): -5.4996 1.0222 48.2706 REMARK 3 T TENSOR REMARK 3 T11: 0.1585 T22: 0.1521 REMARK 3 T33: 0.2202 T12: 0.0061 REMARK 3 T13: -0.0114 T23: -0.0295 REMARK 3 L TENSOR REMARK 3 L11: 1.3011 L22: 1.1365 REMARK 3 L33: 1.1004 L12: 0.2086 REMARK 3 L13: -0.2945 L23: -0.0081 REMARK 3 S TENSOR REMARK 3 S11: -0.0090 S12: 0.1235 S13: -0.0007 REMARK 3 S21: -0.0868 S22: -0.0032 S23: -0.0529 REMARK 3 S31: -0.0134 S32: -0.0140 S33: 0.0149 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'X' AND RESID 91 THROUGH 170) REMARK 3 ORIGIN FOR THE GROUP (A): -3.8495 5.9480 0.8943 REMARK 3 T TENSOR REMARK 3 T11: 0.7662 T22: 0.9003 REMARK 3 T33: 0.2357 T12: 0.0041 REMARK 3 T13: 0.1587 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.6933 L22: 1.0219 REMARK 3 L33: 0.6291 L12: -0.0074 REMARK 3 L13: -0.0651 L23: 0.1288 REMARK 3 S TENSOR REMARK 3 S11: -0.0167 S12: 0.3719 S13: 0.1274 REMARK 3 S21: -0.2401 S22: -0.0795 S23: 0.1677 REMARK 3 S31: -0.4111 S32: -0.1934 S33: 0.0551 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7LFB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000254190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.0 - 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51638 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 49.628 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1FVD REMARK 200 REMARK 200 REMARK: BLOCKS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15%(W/V) PEG 4000, 0.15M AMMONIUM REMARK 280 SULFATE, 0.1M MES PH 6, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.11900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.13100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.11900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.13100 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, X 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH H 523 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 226 LIES ON A SPECIAL POSITION. 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 ASP H 225 REMARK 465 MET X 43 REMARK 465 ASP X 44 REMARK 465 TYR X 45 REMARK 465 LYS X 46 REMARK 465 ASP X 47 REMARK 465 ASP X 48 REMARK 465 ASP X 49 REMARK 465 ASP X 50 REMARK 465 LYS X 51 REMARK 465 GLY X 52 REMARK 465 GLU X 53 REMARK 465 ASN X 54 REMARK 465 LEU X 55 REMARK 465 TYR X 56 REMARK 465 PHE X 57 REMARK 465 GLN X 58 REMARK 465 GLY X 59 REMARK 465 SER X 60 REMARK 465 ASP X 61 REMARK 465 PRO X 62 REMARK 465 GLU X 63 REMARK 465 SER X 64 REMARK 465 SER X 65 REMARK 465 ILE X 66 REMARK 465 PHE X 67 REMARK 465 ILE X 68 REMARK 465 GLU X 69 REMARK 465 ASP X 70 REMARK 465 ALA X 71 REMARK 465 ILE X 72 REMARK 465 LYS X 73 REMARK 465 TYR X 74 REMARK 465 PHE X 75 REMARK 465 LYS X 76 REMARK 465 GLU X 77 REMARK 465 LYS X 78 REMARK 465 VAL X 79 REMARK 465 SER X 80 REMARK 465 THR X 81 REMARK 465 GLN X 82 REMARK 465 ASN X 83 REMARK 465 LEU X 84 REMARK 465 LEU X 85 REMARK 465 LEU X 86 REMARK 465 LEU X 87 REMARK 465 LEU X 88 REMARK 465 THR X 89 REMARK 465 ASP X 90 REMARK 465 GLY X 171 REMARK 465 THR X 172 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 OE1 GLU L 123 O HOH L 401 2.10 REMARK 500 O LYS H 43 OH TYR L 87 2.15 REMARK 500 O HOH L 513 O HOH L 578 2.16 REMARK 500 OG SER L 127 O HOH L 402 2.18 REMARK 500 O PHE H 68 O HOH H 401 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 OE1 GLN X 121 CB ALA X 162 2555 1.94 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 ALA H 28 99.95 -68.31 REMARK 500 ASP H 152 65.05 65.12 REMARK 500 THR H 168 -32.84 -133.07 REMARK 500 ALA L 51 -29.29 73.91 REMARK 500 PRO X 104 49.62 -69.59 REMARK 500 LYS X 127 -20.31 94.86 REMARK 500 ASN X 128 143.65 142.27 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 ASN X 128 TRP X 129 -141.90 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 L 613 DISTANCE = 5.91 ANGSTROMS DBREF 7LFB H 1 225 PDB 7LFB 7LFB 1 225 DBREF 7LFB L 1 214 PDB 7LFB 7LFB 1 214 DBREF 7LFB X 61 172 UNP O14791 APOL1_HUMAN 61 172 SEQADV 7LFB MET X 43 UNP O14791 INITIATING METHIONINE SEQADV 7LFB ASP X 44 UNP O14791 EXPRESSION TAG SEQADV 7LFB TYR X 45 UNP O14791 EXPRESSION TAG SEQADV 7LFB LYS X 46 UNP O14791 EXPRESSION TAG SEQADV 7LFB ASP X 47 UNP O14791 EXPRESSION TAG SEQADV 7LFB ASP X 48 UNP O14791 EXPRESSION TAG SEQADV 7LFB ASP X 49 UNP O14791 EXPRESSION TAG SEQADV 7LFB ASP X 50 UNP O14791 EXPRESSION TAG SEQADV 7LFB LYS X 51 UNP O14791 EXPRESSION TAG SEQADV 7LFB GLY X 52 UNP O14791 EXPRESSION TAG SEQADV 7LFB GLU X 53 UNP O14791 EXPRESSION TAG SEQADV 7LFB ASN X 54 UNP O14791 EXPRESSION TAG SEQADV 7LFB LEU X 55 UNP O14791 EXPRESSION TAG SEQADV 7LFB TYR X 56 UNP O14791 EXPRESSION TAG SEQADV 7LFB PHE X 57 UNP O14791 EXPRESSION TAG SEQADV 7LFB GLN X 58 UNP O14791 EXPRESSION TAG SEQADV 7LFB GLY X 59 UNP O14791 EXPRESSION TAG SEQADV 7LFB SER X 60 UNP O14791 EXPRESSION TAG SEQRES 1 H 225 GLN ILE GLN LEU VAL GLN SER GLY PRO ASP LEU LYS LYS SEQRES 2 H 225 PRO GLY GLU THR VAL LYS ILE SER CYS ARG THR SER GLY SEQRES 3 H 225 TYR ALA PHE THR ASN TYR GLY VAL ASN TRP VAL LYS GLN SEQRES 4 H 225 ALA PRO GLY LYS GLY LEU LYS TRP MET GLY TRP ILE ASN SEQRES 5 H 225 THR ASN THR GLY GLN THR THR TYR ALA GLU GLU PHE ARG SEQRES 6 H 225 GLY ARG PHE ALA ILE SER LEU GLU THR SER ALA SER THR SEQRES 7 H 225 ALA PHE LEU THR ILE SER ASN LEU LYS ASN GLU ASP SER SEQRES 8 H 225 ALA THR TYR PHE CYS ALA ARG LEU ILE TYR ASP GLY ASP SEQRES 9 H 225 TYR ILE SER SER ASP PHE TRP GLY GLN GLY THR THR LEU SEQRES 10 H 225 THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE SEQRES 11 H 225 PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR SEQRES 12 H 225 ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU SEQRES 13 H 225 PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER SEQRES 14 H 225 GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY SEQRES 15 H 225 LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SEQRES 16 H 225 SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS SEQRES 17 H 225 LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO SEQRES 18 H 225 LYS SER CYS ASP SEQRES 1 L 214 ASP ILE GLN MET THR GLN SER PRO ASP SER LEU SER ALA SEQRES 2 L 214 SER VAL GLY GLU THR VAL THR ILE THR CYS GLY ALA SER SEQRES 3 L 214 GLU ASN ILE TYR GLY ALA LEU ASN TRP TYR GLN ARG LYS SEQRES 4 L 214 GLN GLY LYS SER PRO GLN LEU LEU ILE TYR GLY ALA THR SEQRES 5 L 214 ASN LEU ALA ASP GLY MET SER SER ARG PHE SER GLY SER SEQRES 6 L 214 ARG SER GLY ARG GLN TYR SER LEU LYS ILE SER SER LEU SEQRES 7 L 214 HIS PRO ASP ASP VAL ALA THR TYR TYR CYS GLN ASN ALA SEQRES 8 L 214 LEU SER MET PRO TYR THR PHE GLY GLY GLY THR ASN LEU SEQRES 9 L 214 GLU THR LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS SEQRES 1 X 130 MET ASP TYR LYS ASP ASP ASP ASP LYS GLY GLU ASN LEU SEQRES 2 X 130 TYR PHE GLN GLY SER ASP PRO GLU SER SER ILE PHE ILE SEQRES 3 X 130 GLU ASP ALA ILE LYS TYR PHE LYS GLU LYS VAL SER THR SEQRES 4 X 130 GLN ASN LEU LEU LEU LEU LEU THR ASP ASN GLU ALA TRP SEQRES 5 X 130 ASN GLY PHE VAL ALA ALA ALA GLU LEU PRO ARG ASN GLU SEQRES 6 X 130 ALA ASP GLU LEU ARG LYS ALA LEU ASP ASN LEU ALA ARG SEQRES 7 X 130 GLN MET ILE MET LYS ASP LYS ASN TRP HIS ASP LYS GLY SEQRES 8 X 130 GLN GLN TYR ARG ASN TRP PHE LEU LYS GLU PHE PRO ARG SEQRES 9 X 130 LEU LYS SER GLU LEU GLU ASP ASN ILE ARG ARG LEU ARG SEQRES 10 X 130 ALA LEU ALA ASP GLY VAL GLN LYS VAL HIS LYS GLY THR HET GOL H 301 6 HET MES L 301 12 HET SO4 L 302 5 HET SO4 L 303 5 HET GOL L 304 14 HETNAM GOL GLYCEROL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 2(C3 H8 O3) FORMUL 5 MES C6 H13 N O4 S FORMUL 6 SO4 2(O4 S 2-) FORMUL 9 HOH *406(H2 O) HELIX 1 AA1 ALA H 28 TYR H 32 5 5 HELIX 2 AA2 GLU H 62 ARG H 65 5 4 HELIX 3 AA3 THR H 74 ALA H 76 5 3 HELIX 4 AA4 LYS H 87 SER H 91 5 5 HELIX 5 AA5 SER H 135 LYS H 137 5 3 HELIX 6 AA6 SER H 164 ALA H 166 5 3 HELIX 7 AA7 SER H 195 LEU H 197 5 3 HELIX 8 AA8 LYS H 209 ASN H 212 5 4 HELIX 9 AA9 HIS L 79 VAL L 83 5 5 HELIX 10 AB1 SER L 121 SER L 127 1 7 HELIX 11 AB2 LYS L 183 GLU L 187 1 5 HELIX 12 AB3 GLU X 92 GLU X 102 1 11 HELIX 13 AB4 PRO X 104 LYS X 127 1 24 HELIX 14 AB5 LYS X 132 PHE X 144 1 13 HELIX 15 AB6 ARG X 146 GLY X 164 1 19 SHEET 1 AA1 4 GLN H 3 GLN H 6 0 SHEET 2 AA1 4 VAL H 18 SER H 25 -1 O ARG H 23 N VAL H 5 SHEET 3 AA1 4 THR H 78 ILE H 83 -1 O LEU H 81 N ILE H 20 SHEET 4 AA1 4 PHE H 68 GLU H 73 -1 N ALA H 69 O THR H 82 SHEET 1 AA2 6 ASP H 10 LYS H 12 0 SHEET 2 AA2 6 THR H 115 VAL H 119 1 O THR H 118 N LYS H 12 SHEET 3 AA2 6 ALA H 92 TYR H 101 -1 N ALA H 92 O LEU H 117 SHEET 4 AA2 6 GLY H 33 GLN H 39 -1 N GLN H 39 O THR H 93 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O LYS H 46 N LYS H 38 SHEET 6 AA2 6 THR H 58 TYR H 60 -1 O THR H 59 N TRP H 50 SHEET 1 AA3 4 ASP H 10 LYS H 12 0 SHEET 2 AA3 4 THR H 115 VAL H 119 1 O THR H 118 N LYS H 12 SHEET 3 AA3 4 ALA H 92 TYR H 101 -1 N ALA H 92 O LEU H 117 SHEET 4 AA3 4 ILE H 106 TRP H 111 -1 O PHE H 110 N ARG H 98 SHEET 1 AA4 4 SER H 128 LEU H 132 0 SHEET 2 AA4 4 THR H 143 TYR H 153 -1 O GLY H 147 N LEU H 132 SHEET 3 AA4 4 TYR H 184 PRO H 193 -1 O TYR H 184 N TYR H 153 SHEET 4 AA4 4 VAL H 171 THR H 173 -1 N HIS H 172 O VAL H 189 SHEET 1 AA5 4 THR H 139 SER H 140 0 SHEET 2 AA5 4 THR H 143 TYR H 153 -1 O THR H 143 N SER H 140 SHEET 3 AA5 4 TYR H 184 PRO H 193 -1 O TYR H 184 N TYR H 153 SHEET 4 AA5 4 VAL H 177 LEU H 178 -1 N VAL H 177 O SER H 185 SHEET 1 AA6 3 THR H 159 TRP H 162 0 SHEET 2 AA6 3 ILE H 203 HIS H 208 -1 O ASN H 205 N SER H 161 SHEET 3 AA6 3 THR H 213 LYS H 218 -1 O VAL H 215 N VAL H 206 SHEET 1 AA7 4 MET L 4 SER L 7 0 SHEET 2 AA7 4 VAL L 19 ALA L 25 -1 O GLY L 24 N THR L 5 SHEET 3 AA7 4 GLN L 70 ILE L 75 -1 O TYR L 71 N CYS L 23 SHEET 4 AA7 4 PHE L 62 SER L 67 -1 N SER L 67 O GLN L 70 SHEET 1 AA8 6 SER L 10 SER L 14 0 SHEET 2 AA8 6 THR L 102 LYS L 107 1 O ASN L 103 N LEU L 11 SHEET 3 AA8 6 ALA L 84 ASN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 AA8 6 LEU L 33 ARG L 38 -1 N ARG L 38 O THR L 85 SHEET 5 AA8 6 GLN L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA8 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AA9 4 SER L 114 PHE L 118 0 SHEET 2 AA9 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 AA9 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AA9 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 AB1 4 ALA L 153 LEU L 154 0 SHEET 2 AB1 4 ALA L 144 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB1 4 VAL L 191 HIS L 198 -1 O GLU L 195 N GLN L 147 SHEET 4 AB1 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 2 CYS H 148 CYS H 204 1555 1555 2.04 SSBOND 3 CYS H 224 CYS L 214 1555 1555 2.02 SSBOND 4 CYS L 23 CYS L 88 1555 1555 2.05 SSBOND 5 CYS L 134 CYS L 194 1555 1555 2.04 CISPEP 1 PHE H 154 PRO H 155 0 -3.71 CISPEP 2 GLU H 156 PRO H 157 0 1.84 CISPEP 3 SER L 7 PRO L 8 0 -3.68 CISPEP 4 MET L 94 PRO L 95 0 2.47 CISPEP 5 TYR L 140 PRO L 141 0 7.92 CISPEP 6 ASP X 131 LYS X 132 0 0.95 CRYST1 94.238 60.262 124.216 90.00 111.82 90.00 C 1 2 1 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 0.010611 0.000000 0.004248 0.00000 SCALE2 0.000000 0.016594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008672 0.00000