HEADER CELL ADHESION 26-APR-16 5JKD
TITLE CRYSTAL STRUCTURE OF HUMAN IZUMO1-JUNO COMPLEX (CRYSTAL FORM 2)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: IZUMO SPERM-EGG FUSION PROTEIN 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 22-255;
COMPND 5 SYNONYM: OOCYTE BINDING/FUSION FACTOR,OBF,SPERM-SPECIFIC PROTEIN
COMPND 6 IZUMO;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: SPERM-EGG FUSION PROTEIN JUNO;
COMPND 10 CHAIN: B;
COMPND 11 FRAGMENT: UNP RESIDUES 20-228;
COMPND 12 SYNONYM: FOLATE RECEPTOR 4,FOLATE RECEPTOR DELTA,FR-DELTA,IZUMO1
COMPND 13 RECEPTOR PROTEIN JUNO;
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 GENE: IZUMO1;
SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7215;
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 10 ORGANISM_COMMON: HUMAN;
SOURCE 11 ORGANISM_TAXID: 9606;
SOURCE 12 GENE: IZUMO1R, FOLR4, JUNO;
SOURCE 13 EXPRESSION_SYSTEM: DROSOPHILA;
SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7215
KEYWDS FERTILIZATION, IZUMO1, JUNO, CELL ADHESION
EXPDTA X-RAY DIFFRACTION
AUTHOR U.OHTO,H.ISHIDA,T.SHIMIZU
REVDAT 5 08-NOV-23 5JKD 1 HETSYN
REVDAT 4 29-JUL-20 5JKD 1 COMPND REMARK HETNAM LINK
REVDAT 4 2 1 SITE
REVDAT 3 19-FEB-20 5JKD 1 JRNL REMARK
REVDAT 2 29-JUN-16 5JKD 1 JRNL
REVDAT 1 22-JUN-16 5JKD 0
JRNL AUTH U.OHTO,H.ISHIDA,E.KRAYUKHINA,S.UCHIYAMA,N.INOUE,T.SHIMIZU
JRNL TITL STRUCTURE OF IZUMO1-JUNO REVEALS SPERM-OOCYTE RECOGNITION
JRNL TITL 2 DURING MAMMALIAN FERTILIZATION
JRNL REF NATURE V. 534 566 2016
JRNL REFN ESSN 1476-4687
JRNL PMID 27309808
JRNL DOI 10.1038/NATURE18596
REMARK 2
REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0103
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 15006
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.222
REMARK 3 R VALUE (WORKING SET) : 0.220
REMARK 3 FREE R VALUE : 0.251
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 799
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1108
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.82
REMARK 3 BIN R VALUE (WORKING SET) : 0.3620
REMARK 3 BIN FREE R VALUE SET COUNT : 56
REMARK 3 BIN FREE R VALUE : 0.3100
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3480
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 29
REMARK 3 SOLVENT ATOMS : 3
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.92
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -5.40000
REMARK 3 B22 (A**2) : 4.18000
REMARK 3 B33 (A**2) : 1.69000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -1.37000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 1.243
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.358
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.314
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.844
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3622 ; 0.011 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3306 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4920 ; 1.564 ; 1.947
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7654 ; 0.983 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 6.777 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;34.455 ;24.286
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 606 ;17.272 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.595 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 513 ; 0.086 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4035 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 837 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1728 ; 5.061 ; 6.119
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1727 ; 5.062 ; 6.118
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2153 ; 7.874 ; 9.167
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2154 ; 7.872 ; 9.168
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1894 ; 5.919 ; 6.761
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1895 ; 5.918 ; 6.763
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2768 ; 9.269 ; 9.913
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14899 ;14.840 ;58.356
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14899 ;14.839 ;58.361
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 18 A 254
REMARK 3 ORIGIN FOR THE GROUP (A): 36.1337 11.8675 22.4193
REMARK 3 T TENSOR
REMARK 3 T11: 0.1446 T22: 0.3052
REMARK 3 T33: 0.2451 T12: 0.0912
REMARK 3 T13: -0.0192 T23: -0.1396
REMARK 3 L TENSOR
REMARK 3 L11: 1.5587 L22: 0.2415
REMARK 3 L33: 0.7333 L12: -0.3145
REMARK 3 L13: -0.3576 L23: -0.2336
REMARK 3 S TENSOR
REMARK 3 S11: 0.1579 S12: 0.1945 S13: 0.0287
REMARK 3 S21: -0.0192 S22: -0.1533 S23: -0.0032
REMARK 3 S31: -0.0917 S32: -0.0334 S33: -0.0046
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 18 B 230
REMARK 3 ORIGIN FOR THE GROUP (A): 25.6183 -12.2225 7.6791
REMARK 3 T TENSOR
REMARK 3 T11: 0.3496 T22: 0.0843
REMARK 3 T33: 0.1739 T12: -0.0235
REMARK 3 T13: 0.0457 T23: -0.0556
REMARK 3 L TENSOR
REMARK 3 L11: 3.4007 L22: 1.2352
REMARK 3 L33: 1.6845 L12: 1.6579
REMARK 3 L13: 0.8978 L23: 0.9374
REMARK 3 S TENSOR
REMARK 3 S11: -0.0505 S12: -0.2208 S13: 0.0042
REMARK 3 S21: 0.0845 S22: 0.0325 S23: -0.1226
REMARK 3 S31: 0.4692 S32: -0.0424 S33: 0.0180
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5JKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-16.
REMARK 100 THE DEPOSITION ID IS D_1000220778.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-MAR-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : AR-NE3A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15805
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
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 (%) : 99.9
REMARK 200 DATA REDUNDANCY : 6.600
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
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: MOLREP
REMARK 200 STARTING MODEL: 5JK9, 5JKA
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.98
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M (NH4)2SO4, 1.0 M KCL, 0.1 M
REMARK 280 HEPES-NAOH PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 293K
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 72.80200
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.68850
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.80200
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.68850
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2470 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22060 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL
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 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 SER A 68
REMARK 465 LEU A 69
REMARK 465 ASN A 70
REMARK 465 GLU A 71
REMARK 465 ASP A 72
REMARK 465 LYS A 255
REMARK 465 GLU A 256
REMARK 465 PHE A 257
REMARK 465 LEU A 258
REMARK 465 GLU A 259
REMARK 465 VAL A 260
REMARK 465 LEU A 261
REMARK 465 PHE A 262
REMARK 465 GLN A 263
REMARK 465 ARG B 16
REMARK 465 SER B 17
REMARK 465 GLY B 111
REMARK 465 SER B 112
REMARK 465 LEU B 113
REMARK 465 GLY B 114
REMARK 465 TRP B 115
REMARK 465 GLU B 116
REMARK 465 VAL B 117
REMARK 465 ALA B 118
REMARK 465 PRO B 119
REMARK 465 SER B 120
REMARK 465 GLY B 121
REMARK 465 GLN B 122
REMARK 465 LEU B 231
REMARK 465 GLU B 232
REMARK 465 VAL B 233
REMARK 465 LEU B 234
REMARK 465 PHE B 235
REMARK 465 GLN B 236
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 O GLU B 63 OG SER B 69 1.66
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 CYS A 152 18.87 54.90
REMARK 500 THR A 194 -91.76 -121.10
REMARK 500 MET A 222 68.77 38.58
REMARK 500 GLU B 45 -108.44 39.31
REMARK 500 ASN B 53 103.14 -170.66
REMARK 500 HIS B 78 -29.64 -36.22
REMARK 500 LEU B 81 126.17 -38.21
REMARK 500 ARG B 125 -168.22 -126.68
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5JKE RELATED DB: PDB
REMARK 900 RELATED ID: 5JKC RELATED DB: PDB
REMARK 900 RELATED ID: 5JKB RELATED DB: PDB
REMARK 900 RELATED ID: 5JKA RELATED DB: PDB
REMARK 900 RELATED ID: 5JK9 RELATED DB: PDB
DBREF 5JKD A 22 255 UNP Q8IYV9 IZUM1_HUMAN 22 255
DBREF 5JKD B 20 228 UNP A6ND01 JUNO_HUMAN 20 228
SEQADV 5JKD ARG A 18 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD SER A 19 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD PRO A 20 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD TRP A 21 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD GLU A 256 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD PHE A 257 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD LEU A 258 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD GLU A 259 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD VAL A 260 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD LEU A 261 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD PHE A 262 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD GLN A 263 UNP Q8IYV9 EXPRESSION TAG
SEQADV 5JKD ARG B 16 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD SER B 17 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD PRO B 18 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD TRP B 19 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD GLU B 229 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD PHE B 230 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD LEU B 231 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD GLU B 232 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD VAL B 233 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD LEU B 234 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD PHE B 235 UNP A6ND01 EXPRESSION TAG
SEQADV 5JKD GLN B 236 UNP A6ND01 EXPRESSION TAG
SEQRES 1 A 246 ARG SER PRO TRP CYS VAL ILE CYS ASP PRO SER VAL VAL
SEQRES 2 A 246 LEU ALA LEU LYS SER LEU GLU LYS ASP TYR LEU PRO GLY
SEQRES 3 A 246 HIS LEU ASP ALA LYS HIS HIS LYS ALA MET MET GLU ARG
SEQRES 4 A 246 VAL GLU ASN ALA VAL LYS ASP PHE GLN GLU LEU SER LEU
SEQRES 5 A 246 ASN GLU ASP ALA TYR MET GLY VAL VAL ASP GLU ALA THR
SEQRES 6 A 246 LEU GLN LYS GLY SER TRP SER LEU LEU LYS ASP LEU LYS
SEQRES 7 A 246 ARG ILE THR ASP SER ASP VAL LYS GLY ASP LEU PHE VAL
SEQRES 8 A 246 LYS GLU LEU PHE TRP MET LEU HIS LEU GLN LYS GLU THR
SEQRES 9 A 246 PHE ALA THR TYR VAL ALA ARG PHE GLN LYS GLU ALA TYR
SEQRES 10 A 246 CYS PRO ASN LYS CYS GLY VAL MET LEU GLN THR LEU ILE
SEQRES 11 A 246 TRP CYS LYS ASN CYS LYS LYS GLU VAL HIS ALA CYS ARG
SEQRES 12 A 246 LYS SER TYR ASP CYS GLY GLU ARG ASN VAL GLU VAL PRO
SEQRES 13 A 246 GLN MET GLU ASP MET ILE LEU ASP CYS GLU LEU ASN TRP
SEQRES 14 A 246 HIS GLN ALA SER GLU GLY LEU THR ASP TYR SER PHE TYR
SEQRES 15 A 246 ARG VAL TRP GLY ASN ASN THR GLU THR LEU VAL SER LYS
SEQRES 16 A 246 GLY LYS GLU ALA THR LEU THR LYS PRO MET VAL GLY PRO
SEQRES 17 A 246 GLU ASP ALA GLY SER TYR ARG CYS GLU LEU GLY SER VAL
SEQRES 18 A 246 ASN SER SER PRO ALA THR ILE ILE ASN PHE HIS VAL THR
SEQRES 19 A 246 VAL LEU PRO LYS GLU PHE LEU GLU VAL LEU PHE GLN
SEQRES 1 B 221 ARG SER PRO TRP GLY ASP GLU LEU LEU ASN ILE CYS MET
SEQRES 2 B 221 ASN ALA LYS HIS HIS LYS ARG VAL PRO SER PRO GLU ASP
SEQRES 3 B 221 LYS LEU TYR GLU GLU CYS ILE PRO TRP LYS ASP ASN ALA
SEQRES 4 B 221 CYS CYS THR LEU THR THR SER TRP GLU ALA HIS LEU ASP
SEQRES 5 B 221 VAL SER PRO LEU TYR ASN PHE SER LEU PHE HIS CYS GLY
SEQRES 6 B 221 LEU LEU MET PRO GLY CYS ARG LYS HIS PHE ILE GLN ALA
SEQRES 7 B 221 ILE CYS PHE TYR GLU CYS SER PRO ASN LEU GLY PRO TRP
SEQRES 8 B 221 ILE GLN PRO VAL GLY SER LEU GLY TRP GLU VAL ALA PRO
SEQRES 9 B 221 SER GLY GLN GLY GLU ARG VAL VAL ASN VAL PRO LEU CYS
SEQRES 10 B 221 GLN GLU ASP CYS GLU GLU TRP TRP GLU ASP CYS ARG MET
SEQRES 11 B 221 SER TYR THR CYS LYS SER ASN TRP ARG GLY GLY TRP ASP
SEQRES 12 B 221 TRP SER GLN GLY LYS ASN ARG CYS PRO LYS GLY ALA GLN
SEQRES 13 B 221 CYS LEU PRO PHE SER HIS TYR PHE PRO THR PRO ALA ASP
SEQRES 14 B 221 LEU CYS GLU LYS THR TRP SER ASN SER PHE LYS ALA SER
SEQRES 15 B 221 PRO GLU ARG ARG ASN SER GLY ARG CYS LEU GLN LYS TRP
SEQRES 16 B 221 PHE GLU PRO ALA GLN GLY ASN PRO ASN VAL ALA VAL ALA
SEQRES 17 B 221 ARG LEU PHE ALA SER GLU PHE LEU GLU VAL LEU PHE GLN
HET NAG A 300 14
HET NAG B 301 14
HET CL B 302 1
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM CL CHLORIDE ION
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 3 NAG 2(C8 H15 N O6)
FORMUL 5 CL CL 1-
FORMUL 6 HOH *3(H2 O)
HELIX 1 AA1 TRP A 21 CYS A 25 5 5
HELIX 2 AA2 ASP A 26 TYR A 40 1 15
HELIX 3 AA3 TYR A 40 LEU A 45 1 6
HELIX 4 AA4 ASP A 46 LYS A 48 5 3
HELIX 5 AA5 HIS A 49 ASP A 63 1 15
HELIX 6 AA6 ASP A 79 SER A 100 1 22
HELIX 7 AA7 LYS A 103 ALA A 133 1 31
HELIX 8 AA8 LEU A 184 ALA A 189 5 6
HELIX 9 AA9 GLY A 224 ALA A 228 5 5
HELIX 10 AB1 GLY B 20 LEU B 24 5 5
HELIX 11 AB2 TYR B 44 LYS B 51 5 8
HELIX 12 AB3 THR B 57 HIS B 65 1 9
HELIX 13 AB4 LEU B 76 GLY B 80 5 5
HELIX 14 AB5 MET B 83 SER B 100 1 18
HELIX 15 AB6 LEU B 103 PRO B 105 5 3
HELIX 16 AB7 CYS B 132 CYS B 143 1 12
HELIX 17 AB8 PHE B 175 PHE B 179 1 5
HELIX 18 AB9 THR B 181 THR B 189 1 9
HELIX 19 AC1 GLU B 212 GLY B 216 5 5
HELIX 20 AC2 ASN B 219 SER B 228 1 10
SHEET 1 AA1 3 VAL A 77 VAL A 78 0
SHEET 2 AA1 3 GLY A 140 TRP A 148 -1 O ILE A 147 N VAL A 78
SHEET 3 AA1 3 LYS A 154 SER A 162 -1 O CYS A 159 N MET A 142
SHEET 1 AA2 5 GLU A 167 PRO A 173 0
SHEET 2 AA2 5 THR A 244 LEU A 253 1 O HIS A 249 N ARG A 168
SHEET 3 AA2 5 GLY A 229 SER A 237 -1 N CYS A 233 O ILE A 246
SHEET 4 AA2 5 LEU A 193 VAL A 201 -1 N SER A 197 O GLU A 234
SHEET 5 AA2 5 GLU A 207 GLY A 213 -1 O GLY A 213 N TYR A 196
SHEET 1 AA3 2 MET A 178 ASP A 181 0
SHEET 2 AA3 2 THR A 217 LYS A 220 -1 O LYS A 220 N MET A 178
SHEET 1 AA4 2 ILE B 107 GLN B 108 0
SHEET 2 AA4 2 ARG B 125 VAL B 126 -1 O ARG B 125 N GLN B 108
SHEET 1 AA5 2 VAL B 129 LEU B 131 0
SHEET 2 AA5 2 PHE B 194 ALA B 196 1 O LYS B 195 N VAL B 129
SHEET 1 AA6 2 TYR B 147 THR B 148 0
SHEET 2 AA6 2 LEU B 173 PRO B 174 -1 O LEU B 173 N THR B 148
SSBOND 1 CYS A 22 CYS A 149 1555 1555 2.06
SSBOND 2 CYS A 25 CYS A 152 1555 1555 2.07
SSBOND 3 CYS A 135 CYS A 159 1555 1555 2.04
SSBOND 4 CYS A 139 CYS A 165 1555 1555 2.09
SSBOND 5 CYS A 182 CYS A 233 1555 1555 2.01
SSBOND 6 CYS B 27 CYS B 55 1555 1555 2.06
SSBOND 7 CYS B 47 CYS B 95 1555 1555 2.04
SSBOND 8 CYS B 56 CYS B 99 1555 1555 2.03
SSBOND 9 CYS B 79 CYS B 172 1555 1555 2.06
SSBOND 10 CYS B 86 CYS B 143 1555 1555 2.05
SSBOND 11 CYS B 132 CYS B 206 1555 1555 2.08
SSBOND 12 CYS B 136 CYS B 186 1555 1555 2.04
SSBOND 13 CYS B 149 CYS B 166 1555 1555 2.04
LINK ND2 ASN A 204 C1 NAG A 300 1555 1555 1.45
LINK ND2 ASN B 73 C1 NAG B 301 1555 1555 1.44
CRYST1 145.604 65.377 77.199 90.00 104.24 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 0.006868 0.000000 0.001742 0.00000
SCALE2 0.000000 0.015296 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013364 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
