HEADER CELL ADHESION 03-DEC-15 5F4V TITLE CRYSTAL STRUCTURE OF THE HUMAN SPERM IZUMO1 RESIDUES 22-268 COMPND MOL_ID: 1; COMPND 2 MOLECULE: IZUMO SPERM-EGG FUSION PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-268; COMPND 5 SYNONYM: OOCYTE BINDING/FUSION FACTOR,OBF,SPERM-SPECIFIC PROTEIN COMPND 6 IZUMO; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IZUMO1; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7227 KEYWDS GLYCOPROTEIN, MEMBRANE-BOUND, CYSTEINE-RICH, ADHESION, FUSION, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR H.AYDIN,A.SULTANA,J.E.LEE REVDAT 6 27-SEP-23 5F4V 1 HETSYN REVDAT 5 29-JUL-20 5F4V 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 28-DEC-16 5F4V 1 TITLE REVDAT 3 06-JUL-16 5F4V 1 JRNL REVDAT 2 29-JUN-16 5F4V 1 JRNL REVDAT 1 15-JUN-16 5F4V 0 JRNL AUTH H.AYDIN,A.SULTANA,S.LI,A.THAVALINGAM,J.E.LEE JRNL TITL MOLECULAR ARCHITECTURE OF THE HUMAN SPERM IZUMO1 AND EGG JRNL TITL 2 JUNO FERTILIZATION COMPLEX. JRNL REF NATURE V. 534 562 2016 JRNL REFN ESSN 1476-4687 JRNL PMID 27309818 JRNL DOI 10.1038/NATURE18595 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 6482 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.660 REMARK 3 FREE R VALUE TEST SET COUNT : 367 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 47.6090 - 4.1822 1.00 2031 129 0.1707 0.2064 REMARK 3 2 4.1822 - 3.3198 1.00 2060 114 0.1895 0.2328 REMARK 3 3 3.3198 - 2.9002 1.00 2024 124 0.2305 0.2966 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.33 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 : 0.012 1873 REMARK 3 ANGLE : 1.270 2534 REMARK 3 CHIRALITY : 0.055 289 REMARK 3 PLANARITY : 0.006 320 REMARK 3 DIHEDRAL : 15.444 670 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 22 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.5649 45.8374 39.6646 REMARK 3 T TENSOR REMARK 3 T11: 0.3486 T22: 0.3414 REMARK 3 T33: 0.3354 T12: 0.0051 REMARK 3 T13: -0.0199 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 1.8702 L22: 1.2099 REMARK 3 L33: 1.6804 L12: -0.3485 REMARK 3 L13: 1.3998 L23: -1.1245 REMARK 3 S TENSOR REMARK 3 S11: -0.0756 S12: 0.1544 S13: -0.4615 REMARK 3 S21: -0.0955 S22: 0.1742 S23: 0.3675 REMARK 3 S31: -0.0150 S32: -0.3273 S33: -0.1318 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.9731 53.3630 45.2007 REMARK 3 T TENSOR REMARK 3 T11: 0.3198 T22: 0.2641 REMARK 3 T33: 0.2550 T12: -0.0281 REMARK 3 T13: 0.0241 T23: -0.0343 REMARK 3 L TENSOR REMARK 3 L11: 3.3071 L22: 2.2791 REMARK 3 L33: 2.3714 L12: -1.6930 REMARK 3 L13: 1.0590 L23: -0.7239 REMARK 3 S TENSOR REMARK 3 S11: 0.0777 S12: -0.2670 S13: 0.0204 REMARK 3 S21: 0.2388 S22: -0.0339 S23: 0.2163 REMARK 3 S31: 0.0777 S32: -0.1476 S33: -0.0762 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 133 THROUGH 256 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.7244 85.3877 25.2586 REMARK 3 T TENSOR REMARK 3 T11: 0.3199 T22: 0.3793 REMARK 3 T33: 0.2638 T12: -0.0322 REMARK 3 T13: -0.0284 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.5719 L22: 3.3587 REMARK 3 L33: 0.9678 L12: -0.0638 REMARK 3 L13: -0.6293 L23: -0.8508 REMARK 3 S TENSOR REMARK 3 S11: 0.0950 S12: 0.1075 S13: 0.2795 REMARK 3 S21: 0.0576 S22: 0.0570 S23: 0.2423 REMARK 3 S31: -0.1929 S32: -0.0751 S33: -0.1434 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 5F4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-15 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 : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6484 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.603 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 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: 5F4E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.085 M HEPES SODIUM SALT (PH 7.5), REMARK 280 8.5% (V/V) ISOPROPANOL, 17% (W/V) PEG 4000 AND 15% (V/V) REMARK 280 GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 60.65000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.01629 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.80000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 60.65000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 35.01629 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 17.80000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 60.65000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 35.01629 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 17.80000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 70.03259 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 35.60000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 70.03259 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 35.60000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 70.03259 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 35.60000 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 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 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 A 412 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 ILE A 257 REMARK 465 LYS A 258 REMARK 465 GLU A 259 REMARK 465 GLU A 260 REMARK 465 LYS A 261 REMARK 465 PRO A 262 REMARK 465 SER A 263 REMARK 465 PRO A 264 REMARK 465 ASN A 265 REMARK 465 ILE A 266 REMARK 465 VAL A 267 REMARK 465 THR A 268 REMARK 465 GLY A 269 REMARK 465 ARG A 270 REMARK 465 LEU A 271 REMARK 465 VAL A 272 REMARK 465 PRO A 273 REMARK 465 ARG A 274 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 LYS A 51 CG CD CE NZ REMARK 470 ASP A 63 CG OD1 OD2 REMARK 470 ASN A 70 CG OD1 ND2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 GLU A 132 CG CD OE1 OE2 REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 GLN A 174 CG CD OE1 NE2 REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 GLU A 215 CG CD OE1 OE2 REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 MET A 256 CG SD CE 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 NH1 ARG A 232 OE1 GLU A 234 2.17 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 NZ LYS A 85 OD1 ASN A 239 8655 2.03 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 CYS A 22 CB CYS A 22 SG 0.152 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 ASP A 46 CB - CA - C ANGL. DEV. = -19.7 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 HIS A 44 -3.77 -143.43 REMARK 500 LEU A 69 6.65 85.15 REMARK 500 ASN A 70 -128.16 60.28 REMARK 500 GLU A 132 -32.35 -136.69 REMARK 500 LYS A 161 -168.63 -116.38 REMARK 500 THR A 194 -79.56 -116.41 REMARK 500 MET A 222 56.15 35.74 REMARK 500 SER A 240 -162.56 -163.32 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 GLU A 71 ASP A 72 47.11 REMARK 500 VAL A 238 ASN A 239 -46.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F4E RELATED DB: PDB REMARK 900 RELATED ID: 5F4Q RELATED DB: PDB REMARK 900 RELATED ID: 5F4T RELATED DB: PDB DBREF 5F4V A 22 268 UNP Q8IYV9 IZUM1_HUMAN 22 268 SEQADV 5F4V GLY A 269 UNP Q8IYV9 EXPRESSION TAG SEQADV 5F4V ARG A 270 UNP Q8IYV9 EXPRESSION TAG SEQADV 5F4V LEU A 271 UNP Q8IYV9 EXPRESSION TAG SEQADV 5F4V VAL A 272 UNP Q8IYV9 EXPRESSION TAG SEQADV 5F4V PRO A 273 UNP Q8IYV9 EXPRESSION TAG SEQADV 5F4V ARG A 274 UNP Q8IYV9 EXPRESSION TAG SEQRES 1 A 253 CYS VAL ILE CYS ASP PRO SER VAL VAL LEU ALA LEU LYS SEQRES 2 A 253 SER LEU GLU LYS ASP TYR LEU PRO GLY HIS LEU ASP ALA SEQRES 3 A 253 LYS HIS HIS LYS ALA MET MET GLU ARG VAL GLU ASN ALA SEQRES 4 A 253 VAL LYS ASP PHE GLN GLU LEU SER LEU ASN GLU ASP ALA SEQRES 5 A 253 TYR MET GLY VAL VAL ASP GLU ALA THR LEU GLN LYS GLY SEQRES 6 A 253 SER TRP SER LEU LEU LYS ASP LEU LYS ARG ILE THR ASP SEQRES 7 A 253 SER ASP VAL LYS GLY ASP LEU PHE VAL LYS GLU LEU PHE SEQRES 8 A 253 TRP MET LEU HIS LEU GLN LYS GLU THR PHE ALA THR TYR SEQRES 9 A 253 VAL ALA ARG PHE GLN LYS GLU ALA TYR CYS PRO ASN LYS SEQRES 10 A 253 CYS GLY VAL MET LEU GLN THR LEU ILE TRP CYS LYS ASN SEQRES 11 A 253 CYS LYS LYS GLU VAL HIS ALA CYS ARG LYS SER TYR ASP SEQRES 12 A 253 CYS GLY GLU ARG ASN VAL GLU VAL PRO GLN MET GLU ASP SEQRES 13 A 253 MET ILE LEU ASP CYS GLU LEU ASN TRP HIS GLN ALA SER SEQRES 14 A 253 GLU GLY LEU THR ASP TYR SER PHE TYR ARG VAL TRP GLY SEQRES 15 A 253 ASN ASN THR GLU THR LEU VAL SER LYS GLY LYS GLU ALA SEQRES 16 A 253 THR LEU THR LYS PRO MET VAL GLY PRO GLU ASP ALA GLY SEQRES 17 A 253 SER TYR ARG CYS GLU LEU GLY SER VAL ASN SER SER PRO SEQRES 18 A 253 ALA THR ILE ILE ASN PHE HIS VAL THR VAL LEU PRO LYS SEQRES 19 A 253 MET ILE LYS GLU GLU LYS PRO SER PRO ASN ILE VAL THR SEQRES 20 A 253 GLY ARG LEU VAL PRO ARG HET NAG A 301 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 HOH *13(H2 O) HELIX 1 AA1 CYS A 22 CYS A 25 5 4 HELIX 2 AA2 ASP A 26 TYR A 40 1 15 HELIX 3 AA3 LEU A 41 HIS A 44 5 4 HELIX 4 AA4 ASP A 46 ASP A 63 1 18 HELIX 5 AA5 PHE A 64 GLU A 66 5 3 HELIX 6 AA6 GLU A 80 ASP A 101 1 22 HELIX 7 AA7 LYS A 103 ALA A 133 1 31 HELIX 8 AA8 LEU A 184 SER A 190 5 7 HELIX 9 AA9 GLY A 224 ALA A 228 5 5 SHEET 1 AA1 3 VAL A 77 ASP A 79 0 SHEET 2 AA1 3 VAL A 141 TRP A 148 -1 O ILE A 147 N VAL A 78 SHEET 3 AA1 3 LYS A 154 ARG A 160 -1 O HIS A 157 N GLN A 144 SHEET 1 AA2 5 ARG A 168 PRO A 173 0 SHEET 2 AA2 5 SER A 240 LEU A 253 1 O HIS A 249 N ARG A 168 SHEET 3 AA2 5 GLY A 229 SER A 237 -1 N GLY A 229 O VAL A 250 SHEET 4 AA2 5 LEU A 193 VAL A 201 -1 N TYR A 199 O ARG A 232 SHEET 5 AA2 5 GLU A 207 GLY A 213 -1 O VAL A 210 N PHE A 198 SHEET 1 AA3 2 MET A 178 ASP A 181 0 SHEET 2 AA3 2 THR A 217 LYS A 220 -1 O LEU A 218 N LEU A 180 SSBOND 1 CYS A 22 CYS A 149 1555 1555 2.07 SSBOND 2 CYS A 25 CYS A 152 1555 1555 2.05 SSBOND 3 CYS A 135 CYS A 159 1555 1555 2.06 SSBOND 4 CYS A 139 CYS A 165 1555 1555 2.11 SSBOND 5 CYS A 182 CYS A 233 1555 1555 1.93 LINK ND2 ASN A 204 C1 NAG A 301 1555 1555 1.46 CRYST1 121.300 121.300 53.400 90.00 90.00 120.00 H 3 9 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 0.008244 0.004760 0.000000 0.00000 SCALE2 0.000000 0.009519 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018727 0.00000