HEADER IMMUNE SYSTEM 03-MAY-20 6YXK TITLE CRYSTAL STRUCTURE OF ACPA 3F3 IN COMPLEX WITH CIT-VIMENTIN 59-74 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACPA 3F3 FAB FRAGMENT - HEAVY CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ACPA 3F3 FAB FRAGMENT - LIGHT CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CITRULLINATED VIMENTIN (59-74); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: EXPI 293F(TM); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PCEP4; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM_CELL_LINE: EXPI 293F(TM); SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PCEP4; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606 KEYWDS ANTI-CITRULLINATED PROTEIN ANTIBODY FAB FRAGMENT, CITRULLINATED KEYWDS 2 VIMENTIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.GE,R.HOLMDAHL REVDAT 4 24-JAN-24 6YXK 1 REMARK REVDAT 3 15-NOV-23 6YXK 1 REMARK LINK ATOM REVDAT 2 25-MAY-22 6YXK 1 JRNL REVDAT 1 12-MAY-21 6YXK 0 JRNL AUTH T.KISSEL,C.GE,L.HAFKENSCHEID,J.C.KWEKKEBOOM,L.M.SLOT, JRNL AUTH 2 M.CAVALLARI,Y.HE,K.A.VAN SCHIE,R.D.VERGROESEN, JRNL AUTH 3 A.S.B.KAMPSTRA,S.REIJM,G.STOEKEN-RIJSBERGEN,C.KOELEMAN, JRNL AUTH 4 L.M.VOORTMAN,L.H.HEITMAN,B.XU,G.J.M.PRUIJN,M.WUHRER, JRNL AUTH 5 T.RISPENS,T.W.J.HUIZINGA,H.U.SCHERER,M.RETH,R.HOLMDAHL, JRNL AUTH 6 R.E.M.TOES JRNL TITL SURFACE IG VARIABLE DOMAIN GLYCOSYLATION AFFECTS AUTOANTIGEN JRNL TITL 2 BINDING AND ACTS AS THRESHOLD FOR HUMAN AUTOREACTIVE B CELL JRNL TITL 3 ACTIVATION. JRNL REF SCI ADV V. 8 M1759 2022 JRNL REFN ESSN 2375-2548 JRNL PMID 35138894 JRNL DOI 10.1126/SCIADV.ABM1759 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 40902 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.953 REMARK 3 FREE R VALUE TEST SET COUNT : 2026 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3417 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.92600 REMARK 3 B22 (A**2) : -1.27500 REMARK 3 B33 (A**2) : 2.20100 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): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.327 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3546 ; 0.018 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3151 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4819 ; 2.259 ; 1.665 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7356 ; 1.472 ; 1.597 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 439 ; 8.140 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;34.069 ;23.660 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 546 ;15.786 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.968 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 469 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3939 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 728 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 631 ; 0.240 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 39 ; 0.272 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1711 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 289 ; 0.192 ; 0.200 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): 1774 ; 1.344 ; 1.670 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1773 ; 1.344 ; 1.669 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2207 ; 2.051 ; 2.490 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2208 ; 2.051 ; 2.492 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1772 ; 1.842 ; 1.877 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1772 ; 1.838 ; 1.877 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2612 ; 2.821 ; 2.731 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2613 ; 2.821 ; 2.731 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 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 2 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): 14.4399 65.3707 23.8700 REMARK 3 T TENSOR REMARK 3 T11: 0.2158 T22: 0.2182 REMARK 3 T33: 0.0201 T12: -0.0299 REMARK 3 T13: -0.0010 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.5688 L22: 1.4885 REMARK 3 L33: 0.8003 L12: -0.7938 REMARK 3 L13: 0.7003 L23: -0.5057 REMARK 3 S TENSOR REMARK 3 S11: -0.0541 S12: -0.0435 S13: 0.1757 REMARK 3 S21: 0.0438 S22: -0.0148 S23: -0.0868 REMARK 3 S31: -0.0944 S32: -0.0429 S33: 0.0689 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 1 B 301 REMARK 3 ORIGIN FOR THE GROUP (A): 4.1662 54.3933 13.8032 REMARK 3 T TENSOR REMARK 3 T11: 0.2272 T22: 0.2461 REMARK 3 T33: 0.0128 T12: -0.0330 REMARK 3 T13: -0.0058 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.8521 L22: 1.2336 REMARK 3 L33: 1.0330 L12: -0.8414 REMARK 3 L13: 0.7249 L23: -0.9711 REMARK 3 S TENSOR REMARK 3 S11: 0.0566 S12: 0.0283 S13: -0.0825 REMARK 3 S21: -0.0538 S22: 0.0339 S23: 0.1217 REMARK 3 S31: 0.0083 S32: -0.0437 S33: -0.0905 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 9 REMARK 3 ORIGIN FOR THE GROUP (A): 30.7698 35.8474 32.7920 REMARK 3 T TENSOR REMARK 3 T11: 0.1706 T22: 0.1841 REMARK 3 T33: 0.1694 T12: 0.0063 REMARK 3 T13: -0.0087 T23: 0.0195 REMARK 3 L TENSOR REMARK 3 L11: 0.0358 L22: 8.3666 REMARK 3 L33: 1.3503 L12: -0.4656 REMARK 3 L13: 0.2133 L23: -2.3901 REMARK 3 S TENSOR REMARK 3 S11: -0.0021 S12: 0.0411 S13: 0.0170 REMARK 3 S21: 0.0197 S22: -0.0375 S23: -0.4407 REMARK 3 S31: 0.0199 S32: 0.3112 S33: 0.0397 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 6YXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292108465. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-18 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 : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91840 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 0.7.4 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40933 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 52.334 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 52.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.05800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 STARTING MODEL: 5OCX(EARLY MODEL) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS PH 7.5, 20MM NACL, 0.2M REMARK 280 AMMONIUM CHLORIDE PH 6.3, (20%) W/V PEG 3350), VAPOR DIFFUSION, REMARK 280 SITTING 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 26.68950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.80650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.04700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.80650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.68950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.04700 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: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 THR A 141 REMARK 465 SER A 142 REMARK 465 GLY A 143 REMARK 465 GLY C -5 REMARK 465 VAL C -4 REMARK 465 TYR C -3 REMARK 465 ALA C -2 REMARK 465 THR C -1 REMARK 465 ARG C 0 REMARK 465 VAL C 10 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 ND2 ASN B 78 H1 NAG B 301 0.67 REMARK 500 C VAL C 4 H CIR C 5 0.91 REMARK 500 HD21 ASN B 78 H1 NAG B 301 0.98 REMARK 500 HD1 HIS A 35 HE1 TRP A 47 1.10 REMARK 500 C LEU C 6 H CIR C 7 1.41 REMARK 500 C GLY B 105 HG3 GLN B 106 1.55 REMARK 500 C LEU C 6 H2 CIR C 7 1.56 REMARK 500 O HOH A 429 O HOH A 529 1.87 REMARK 500 O HOH A 412 O HOH A 534 2.10 REMARK 500 O LYS A 139 O HOH A 401 2.16 REMARK 500 O HOH A 529 O HOH A 535 2.17 REMARK 500 O6 NAG A 302 O HOH A 402 2.18 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 GLN B 106 N GLN B 106 CA 0.132 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 PRO A 159 N - CA - CB ANGL. DEV. = -8.0 DEGREES REMARK 500 GLY B 105 CA - C - O ANGL. DEV. = -13.2 DEGREES REMARK 500 GLN B 106 N - CA - CB ANGL. DEV. = -19.8 DEGREES REMARK 500 GLN B 106 CA - C - N ANGL. DEV. = 13.3 DEGREES REMARK 500 GLN B 106 O - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 ARG B 109 CG - CD - NE ANGL. DEV. = -22.7 DEGREES REMARK 500 CYS B 199 CA - CB - SG ANGL. DEV. = -13.3 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 LEU A 43 -169.18 -118.87 REMARK 500 SER A 138 36.32 -78.62 REMARK 500 SER B 57 -44.13 83.16 REMARK 500 ALA B 90 173.50 179.26 REMARK 500 GLN B 106 117.43 -168.38 REMARK 500 ASN B 143 63.81 61.55 REMARK 500 LYS B 195 -60.35 -98.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CIR C 7 10.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 6YXK A 2 224 PDB 6YXK 6YXK 2 224 DBREF 6YXK B 1 218 PDB 6YXK 6YXK 1 218 DBREF 6YXK C -5 10 UNP P08670 VIME_HUMAN 59 74 SEQRES 1 A 223 VAL GLN LEU VAL GLN PRO GLY ALA GLU VAL MET GLN PRO SEQRES 2 A 223 GLY ALA SER MET LYS VAL PRO CYS GLU THR SER GLY TYR SEQRES 3 A 223 ILE PHE ASN ASP TYR TYR LEU HIS TRP VAL ARG GLN ALA SEQRES 4 A 223 PRO GLY LEU GLY LEU GLU TRP MET GLY TRP ILE ALA PRO SEQRES 5 A 223 LYS THR GLY VAL THR LYS PHE ALA GLN LYS PHE GLN GLY SEQRES 6 A 223 ARG VAL ASN MET THR ALA ASP SER SER VAL ASN THR SER SEQRES 7 A 223 TYR LEU GLU MET THR GLY LEU THR PHE ASP ASP THR ALA SEQRES 8 A 223 VAL TYR PHE CYS ALA ARG GLY THR TYR LEU PRO VAL ASP SEQRES 9 A 223 GLU SER ALA ALA PHE ASP VAL TRP GLY LEU GLY THR ASP SEQRES 10 A 223 VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL SEQRES 11 A 223 PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY SEQRES 12 A 223 THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO SEQRES 13 A 223 GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SEQRES 14 A 223 SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER SEQRES 15 A 223 GLY LEU PHE SER LEU SER SER VAL VAL THR VAL PRO SER SEQRES 16 A 223 SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN SEQRES 17 A 223 HIS LYS PRO SER ASN THR LYS VAL ASP LYS ARG VAL GLU SEQRES 18 A 223 PRO LYS SEQRES 1 B 218 ASP ILE GLU MET THR GLN TYR PRO ASP SER LEU ALA VAL SEQRES 2 B 218 PHE LEU GLY GLU ARG ALA THR VAL ASN CYS LYS SER SER SEQRES 3 B 218 GLN SER VAL LEU HIS TRP GLY ASN ASP LYS ASN TYR PHE SEQRES 4 B 218 ALA TRP TYR GLN GLN LYS ARG GLY GLN ALA PRO LYS LEU SEQRES 5 B 218 LEU ILE SER SER SER SER ALA ARG GLU SER GLY VAL PRO SEQRES 6 B 218 ASP ARG PHE SER GLY SER GLY SER GLY THR ASP PHE ASN SEQRES 7 B 218 LEU THR ILE SER SER LEU GLN ALA GLU ASP VAL ALA VAL SEQRES 8 B 218 TYR PHE CYS GLN GLN TYR TYR GLU ALA PRO TYR THR PHE SEQRES 9 B 218 GLY GLN GLY THR ARG LEU GLU ILE LYS THR VAL ALA ALA SEQRES 10 B 218 PRO SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU SEQRES 11 B 218 LYS SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN SEQRES 12 B 218 PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP SEQRES 13 B 218 ASN ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR SEQRES 14 B 218 GLU GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER SEQRES 15 B 218 THR LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS SEQRES 16 B 218 VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER SEQRES 17 B 218 PRO VAL THR LYS SER PHE ASN ARG GLY CYS SEQRES 1 C 16 GLY VAL TYR ALA THR ARG SER SER ALA VAL CIR LEU CIR SEQRES 2 C 16 SER SER VAL MODRES 6YXK CIR C 5 ARG MODIFIED RESIDUE MODRES 6YXK CIR C 7 ARG MODIFIED RESIDUE HET CIR C 5 23 HET CIR C 7 23 HET NAG A 301 28 HET NAG A 302 28 HET NAG B 301 28 HETNAM CIR CITRULLINE 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 3 CIR 2(C6 H13 N3 O3) FORMUL 4 NAG 3(C8 H15 N O6) FORMUL 7 HOH *303(H2 O) HELIX 1 AA1 ILE A 28 ASN A 30 5 3 HELIX 2 AA2 GLN A 62 GLN A 65 5 4 HELIX 3 AA3 SER A 74 VAL A 76 5 3 HELIX 4 AA4 THR A 87 THR A 91 5 5 HELIX 5 AA5 SER A 166 ALA A 168 5 3 HELIX 6 AA6 SER A 197 LEU A 199 5 3 HELIX 7 AA7 LYS A 211 ASN A 214 5 4 HELIX 8 AA8 GLN B 85 VAL B 89 5 5 HELIX 9 AA9 SER B 126 SER B 132 1 7 HELIX 10 AB1 LYS B 188 GLU B 192 1 5 SHEET 1 AA1 4 GLN A 3 VAL A 5 0 SHEET 2 AA1 4 MET A 18 SER A 25 -1 O GLU A 23 N VAL A 5 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O LEU A 81 N VAL A 20 SHEET 4 AA1 4 VAL A 68 ASP A 73 -1 N ASP A 73 O THR A 78 SHEET 1 AA2 6 ALA A 9 MET A 12 0 SHEET 2 AA2 6 THR A 117 VAL A 121 1 O THR A 120 N MET A 12 SHEET 3 AA2 6 ALA A 92 TYR A 101 -1 N ALA A 92 O VAL A 119 SHEET 4 AA2 6 TYR A 32 GLN A 39 -1 N VAL A 37 O PHE A 95 SHEET 5 AA2 6 GLU A 46 ALA A 52 -1 O MET A 48 N TRP A 36 SHEET 6 AA2 6 VAL A 57 PHE A 60 -1 O LYS A 59 N TRP A 50 SHEET 1 AA3 4 ALA A 9 MET A 12 0 SHEET 2 AA3 4 THR A 117 VAL A 121 1 O THR A 120 N MET A 12 SHEET 3 AA3 4 ALA A 92 TYR A 101 -1 N ALA A 92 O VAL A 119 SHEET 4 AA3 4 VAL A 112 TRP A 113 -1 O VAL A 112 N ARG A 98 SHEET 1 AA4 4 SER A 130 LEU A 134 0 SHEET 2 AA4 4 THR A 145 TYR A 155 -1 O LEU A 151 N PHE A 132 SHEET 3 AA4 4 PHE A 186 PRO A 195 -1 O PHE A 186 N TYR A 155 SHEET 4 AA4 4 VAL A 173 THR A 175 -1 N HIS A 174 O VAL A 191 SHEET 1 AA5 4 SER A 130 LEU A 134 0 SHEET 2 AA5 4 THR A 145 TYR A 155 -1 O LEU A 151 N PHE A 132 SHEET 3 AA5 4 PHE A 186 PRO A 195 -1 O PHE A 186 N TYR A 155 SHEET 4 AA5 4 VAL A 179 LEU A 180 -1 N VAL A 179 O SER A 187 SHEET 1 AA6 3 THR A 161 TRP A 164 0 SHEET 2 AA6 3 ILE A 205 HIS A 210 -1 O ASN A 207 N SER A 163 SHEET 3 AA6 3 THR A 215 ARG A 220 -1 O VAL A 217 N VAL A 208 SHEET 1 AA7 4 MET B 4 TYR B 7 0 SHEET 2 AA7 4 ALA B 19 SER B 25 -1 O ASN B 22 N TYR B 7 SHEET 3 AA7 4 ASP B 76 ILE B 81 -1 O ILE B 81 N ALA B 19 SHEET 4 AA7 4 PHE B 68 SER B 73 -1 N SER B 69 O THR B 80 SHEET 1 AA8 6 SER B 10 VAL B 13 0 SHEET 2 AA8 6 GLY B 107 GLU B 111 1 O THR B 108 N LEU B 11 SHEET 3 AA8 6 ALA B 90 GLN B 96 -1 N TYR B 92 O GLY B 107 SHEET 4 AA8 6 PHE B 39 GLN B 44 -1 N TYR B 42 O PHE B 93 SHEET 5 AA8 6 LYS B 51 SER B 55 -1 O LEU B 53 N TRP B 41 SHEET 6 AA8 6 ALA B 59 ARG B 60 -1 O ALA B 59 N SER B 55 SHEET 1 AA9 4 SER B 119 PHE B 123 0 SHEET 2 AA9 4 THR B 134 PHE B 144 -1 O ASN B 142 N SER B 119 SHEET 3 AA9 4 TYR B 178 SER B 187 -1 O TYR B 178 N PHE B 144 SHEET 4 AA9 4 SER B 164 VAL B 168 -1 N GLN B 165 O THR B 183 SHEET 1 AB1 4 ALA B 158 LEU B 159 0 SHEET 2 AB1 4 LYS B 150 VAL B 155 -1 N VAL B 155 O ALA B 158 SHEET 3 AB1 4 VAL B 196 THR B 202 -1 O GLU B 200 N GLN B 152 SHEET 4 AB1 4 VAL B 210 ASN B 215 -1 O VAL B 210 N VAL B 201 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.13 SSBOND 2 CYS A 150 CYS A 206 1555 1555 2.16 SSBOND 3 CYS B 23 CYS B 94 1555 1555 2.21 SSBOND 4 CYS B 139 CYS B 199 1555 1555 2.01 LINK ND2 ASN A 69 C1 NAG A 301 1555 1555 1.49 LINK ND2 ASN A 77 C1 NAG A 302 1555 1555 1.46 LINK ND2 ASN B 78 C1 NAG B 301 1555 1555 1.47 LINK C VAL C 4 N CIR C 5 1555 1555 1.38 LINK C CIR C 5 N LEU C 6 1555 1555 1.31 LINK C LEU C 6 N CIR C 7 1555 1555 1.30 LINK C CIR C 7 N SER C 8 1555 1555 1.38 CISPEP 1 PHE A 156 PRO A 157 0 -9.35 CISPEP 2 GLU A 158 PRO A 159 0 -5.48 CISPEP 3 TYR B 7 PRO B 8 0 -5.77 CISPEP 4 ALA B 100 PRO B 101 0 -5.38 CISPEP 5 TYR B 145 PRO B 146 0 -5.88 CRYST1 53.379 82.094 135.613 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 0.018734 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007374 0.00000