HEADER IMMUNE SYSTEM 05-JUL-24 9CJ0 TITLE THE HIGH-RESOLUTION STRUCTURE OF A VARIABLE LYMPHOCYTE RECEPTOR FROM TITLE 2 PETROMYZON MARINUS CAPABLE OF BINDING TO THE BRAIN EXTRACELLULAR TITLE 3 MATRIX COMPND MOL_ID: 1; COMPND 2 MOLECULE: VARIABLE LYMPHOCYTE RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PETROMYZON MARINUS; SOURCE 3 ORGANISM_TAXID: 7757; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: SHUFFLE T7 EXPRESS KEYWDS ADAPTIVE IMMUNE SYSTEM OF JAWLESS VERTEBRATES, ALTERNATIVE ANTIGEN KEYWDS 2 RECEPTOR, LEUCINE-RICH REPEAT, VARIABLE LYMPHOCYTE RECEPTOR, VLR KEYWDS 3 TECHNOLOGIES, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR E.A.APPELT,J.B.THODEN,E.V.SHUSTA,H.M.HOLDEN REVDAT 2 04-SEP-24 9CJ0 1 TITLE JRNL REVDAT 1 31-JUL-24 9CJ0 0 JRNL AUTH E.A.APPELT,J.B.THODEN,S.A.GEHRKE,H.D.BACHMEIER,I.RAYMENT, JRNL AUTH 2 H.M.HOLDEN,E.V.SHUSTA JRNL TITL THE HIGH-RESOLUTION STRUCTURE OF A VARIABLE LYMPHOCYTE JRNL TITL 2 RECEPTOR FROM PETROMYZON MARINUS CAPABLE OF BINDING TO THE JRNL TITL 3 BRAIN EXTRACELLULAR MATRIX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 34487 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1720 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2301 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1315 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.058 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.063 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.222 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1431 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1360 ; 0.000 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1969 ; 1.636 ; 1.639 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3160 ; 1.431 ; 1.577 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 189 ; 7.518 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 62 ;36.445 ;22.581 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 244 ;14.928 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;17.776 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 193 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1599 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 311 ; 0.001 ; 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): 699 ; 1.766 ; 1.504 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 698 ; 1.762 ; 1.497 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 877 ; 2.719 ; 2.240 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 878 ; 2.718 ; 2.248 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 732 ; 2.523 ; 1.779 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 725 ; 2.469 ; 1.753 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1071 ; 3.818 ; 2.521 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1643 ; 5.597 ;18.763 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1600 ; 5.455 ;18.180 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 9CJ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000285664. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36207 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42000 REMARK 200 FOR SHELL : 3.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5-2.8 M AMMONIUM SULFATE, 2% REMARK 280 HEXYLENEGLYCOL, 100 MM HEPPS (PH 8), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 22.76100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.17400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.56850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.17400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.76100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.56850 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 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 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 HOH A 329 O HOH A 379 1.91 REMARK 500 NH1 ARG A 35 O3 SO4 A 203 2.05 REMARK 500 O HOH A 368 O HOH A 461 2.11 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 GLN A 10 -116.86 51.43 REMARK 500 SER A 38 63.45 62.68 REMARK 500 SER A 38 64.88 61.04 REMARK 500 ASN A 63 -160.34 -127.44 REMARK 500 LEU A 76 54.66 -93.80 REMARK 500 REMARK 500 REMARK: NULL DBREF 9CJ0 A -1 168 PDB 9CJ0 9CJ0 -1 168 SEQRES 1 A 170 GLY HIS ALA CYS PRO SER GLN CYS SER CYS ASP GLN THR SEQRES 2 A 170 THR VAL LYS CYS HIS SER ARG ARG LEU THR SER VAL PRO SEQRES 3 A 170 ALA GLY ILE PRO THR THR THR LYS ILE LEU ARG LEU TYR SEQRES 4 A 170 SER ASN GLN ILE THR LYS LEU GLU PRO GLY VAL PHE ASP SEQRES 5 A 170 HIS LEU VAL ASN LEU GLU LYS LEU TYR ILE SER TRP ASN SEQRES 6 A 170 GLN LEU SER ALA LEU PRO VAL GLY VAL PHE ASP LYS LEU SEQRES 7 A 170 THR LYS LEU THR HIS LEU SER LEU GLY TYR ASN GLN LEU SEQRES 8 A 170 LYS SER VAL PRO ARG GLY ALA PHE ASP ASN LEU LYS SER SEQRES 9 A 170 LEU THR HIS ILE TRP LEU LEU ASN ASN PRO TRP ASP CYS SEQRES 10 A 170 GLU CYS SER ASP ILE LEU TYR LEU LYS ASN TRP ILE VAL SEQRES 11 A 170 GLN HIS ALA SER ILE VAL ASN LEU GLN GLY HIS GLY GLY SEQRES 12 A 170 VAL ASP ASN VAL LYS CYS SER GLY THR ASN THR PRO VAL SEQRES 13 A 170 ARG ALA VAL THR GLU ALA SER THR SER PRO SER LYS CYS SEQRES 14 A 170 PRO HET EP1 A 201 16 HET SO4 A 202 5 HET SO4 A 203 5 HETNAM EP1 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC HETNAM 2 EP1 ACID HETNAM SO4 SULFATE ION FORMUL 2 EP1 C9 H20 N2 O4 S FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *179(H2 O) HELIX 1 AA1 CYS A 117 ASP A 119 5 3 HELIX 2 AA2 ILE A 120 HIS A 130 1 11 HELIX 3 AA3 ALA A 131 VAL A 134 5 4 HELIX 4 AA4 GLY A 141 VAL A 145 5 5 HELIX 5 AA5 PRO A 153 VAL A 157 5 5 HELIX 6 AA6 THR A 158 THR A 162 5 5 HELIX 7 AA7 SER A 163 CYS A 167 5 5 SHEET 1 AA1 6 SER A 7 ASP A 9 0 SHEET 2 AA1 6 THR A 12 LYS A 14 -1 O LYS A 14 N SER A 7 SHEET 3 AA1 6 ILE A 33 ARG A 35 1 O ILE A 33 N VAL A 13 SHEET 4 AA1 6 LYS A 57 TYR A 59 1 O LYS A 57 N LEU A 34 SHEET 5 AA1 6 HIS A 81 SER A 83 1 O SER A 83 N LEU A 58 SHEET 6 AA1 6 HIS A 105 TRP A 107 1 O TRP A 107 N LEU A 82 SSBOND 1 CYS A 2 CYS A 8 1555 1555 2.06 SSBOND 2 CYS A 6 CYS A 15 1555 1555 2.05 SSBOND 3 CYS A 115 CYS A 147 1555 1555 2.03 SSBOND 4 CYS A 117 CYS A 167 1555 1555 2.05 CRYST1 45.522 53.137 60.348 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 0.021967 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016571 0.00000