HEADER VIRAL PROTEIN 14-FEB-23 8IDO TITLE CRYSTAL STRUCTURE OF NANOBODY VHH-T148 WITH MERS-COV RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VHH-T148; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MIDDLE EAST RESPIRATORY SYNDROME-RELATED SOURCE 3 CORONAVIRUS; SOURCE 4 ORGANISM_COMMON: MERS-COV; SOURCE 5 ORGANISM_TAXID: 1335626; SOURCE 6 GENE: S; SOURCE 7 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: CAMELUS DROMEDARIUS; SOURCE 11 ORGANISM_TAXID: 9838; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS MERS-COV, NANOBODY, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,L.TIAN REVDAT 1 28-FEB-24 8IDO 0 JRNL AUTH L.TIAN,R.WANG,L.ZHANG,X.WANG JRNL TITL STRUCTURES AND NEUTRALIZING MECHANISMS OF CAMEL NANOBODIES JRNL TITL 2 TARGETING THE RECEPTOR-BINDING DOMAIN OF MERS-COV SPIKE JRNL TITL 3 GLYCOPROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 36418 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1828 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 2.5676 - 2.5002 0.96 2491 124 0.2660 0.3280 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.008 5229 REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 392.1222 66.7467 153.3792 REMARK 3 T TENSOR REMARK 3 T11: 0.3901 T22: 0.4318 REMARK 3 T33: 0.3382 T12: -0.0483 REMARK 3 T13: 0.0400 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.5533 L22: 0.7814 REMARK 3 L33: 0.2787 L12: -0.0812 REMARK 3 L13: 0.1842 L23: 0.1086 REMARK 3 S TENSOR REMARK 3 S11: 0.0043 S12: -0.3058 S13: -0.0215 REMARK 3 S21: 0.1633 S22: -0.0555 S23: 0.1056 REMARK 3 S31: -0.0425 S32: -0.0859 S33: 0.0127 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 8IDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 21-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-20 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36441 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 16.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 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 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% V/V TACSIMATE PH 6.0, 12% W/V PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 87.94800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.59500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 87.94800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.59500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: B, D, E 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, F 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 C 235 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 GLU B 367 REMARK 465 ALA B 368 REMARK 465 LYS B 369 REMARK 465 PRO B 370 REMARK 465 SER B 371 REMARK 465 GLY B 372 REMARK 465 SER B 373 REMARK 465 VAL B 374 REMARK 465 VAL B 375 REMARK 465 GLU B 376 REMARK 465 GLN B 377 REMARK 465 ALA B 378 REMARK 465 GLU B 379 REMARK 465 GLY B 380 REMARK 465 ARG B 505 REMARK 465 LEU B 506 REMARK 465 LEU B 507 REMARK 465 SER B 508 REMARK 465 ASP B 509 REMARK 465 ASP B 510 REMARK 465 ARG B 511 REMARK 465 THR B 512 REMARK 465 GLU B 513 REMARK 465 GLN B 544 REMARK 465 LEU B 545 REMARK 465 SER B 546 REMARK 465 PRO B 547 REMARK 465 LEU B 548 REMARK 465 GLU B 549 REMARK 465 GLY B 550 REMARK 465 GLY B 551 REMARK 465 GLY B 552 REMARK 465 TRP B 553 REMARK 465 LEU B 554 REMARK 465 GLU B 589 REMARK 465 HIS B 590 REMARK 465 HIS B 591 REMARK 465 HIS B 592 REMARK 465 HIS B 593 REMARK 465 HIS B 594 REMARK 465 HIS B 595 REMARK 465 GLU A 367 REMARK 465 ALA A 368 REMARK 465 LYS A 369 REMARK 465 PRO A 370 REMARK 465 SER A 371 REMARK 465 GLY A 372 REMARK 465 SER A 373 REMARK 465 VAL A 374 REMARK 465 VAL A 375 REMARK 465 GLU A 376 REMARK 465 GLN A 377 REMARK 465 ALA A 378 REMARK 465 GLU A 379 REMARK 465 GLY A 380 REMARK 465 GLU A 589 REMARK 465 HIS A 590 REMARK 465 HIS A 591 REMARK 465 HIS A 592 REMARK 465 HIS A 593 REMARK 465 HIS A 594 REMARK 465 HIS A 595 REMARK 465 SER C 129 REMARK 465 HIS C 130 REMARK 465 HIS C 131 REMARK 465 HIS C 132 REMARK 465 HIS C 133 REMARK 465 HIS C 134 REMARK 465 HIS C 135 REMARK 465 GLN D 1 REMARK 465 SER D 129 REMARK 465 HIS D 130 REMARK 465 HIS D 131 REMARK 465 HIS D 132 REMARK 465 HIS D 133 REMARK 465 HIS D 134 REMARK 465 HIS D 135 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 NZ LYS C 110 O HOH C 201 1.20 REMARK 500 OH TYR A 540 O HOH A 601 1.94 REMARK 500 O HOH B 645 O HOH B 665 1.95 REMARK 500 O HOH A 644 O HOH A 660 1.98 REMARK 500 O HOH A 605 O HOH A 701 2.01 REMARK 500 O HOH B 654 O HOH B 661 2.01 REMARK 500 O HOH A 677 O HOH A 694 2.02 REMARK 500 O GLY D 122 O HOH D 201 2.02 REMARK 500 O HOH A 742 O HOH A 743 2.03 REMARK 500 O HOH B 671 O HOH B 681 2.03 REMARK 500 O TRP D 103 O HOH D 202 2.03 REMARK 500 O HOH B 650 O HOH B 664 2.04 REMARK 500 O HOH A 672 O HOH A 699 2.06 REMARK 500 O HOH A 736 O HOH A 739 2.06 REMARK 500 O HOH B 617 O HOH B 659 2.11 REMARK 500 O HOH A 637 O HOH A 665 2.11 REMARK 500 O HOH D 218 O HOH D 220 2.12 REMARK 500 O LEU A 588 O HOH A 602 2.12 REMARK 500 O HOH D 206 O HOH D 218 2.12 REMARK 500 O HOH B 679 O HOH B 684 2.15 REMARK 500 O3 BMA F 3 C2 MAN F 4 2.17 REMARK 500 O3 BMA E 3 O5 MAN E 4 2.17 REMARK 500 O HOH A 646 O HOH A 711 2.17 REMARK 500 O ARG B 542 O HOH B 601 2.17 REMARK 500 NZ LYS C 19 O HOH C 202 2.18 REMARK 500 O HOH A 622 O HOH A 667 2.18 REMARK 500 O HOH C 227 O HOH C 234 2.18 REMARK 500 O HOH B 627 O HOH B 660 2.18 REMARK 500 O HOH A 671 O HOH A 729 2.18 REMARK 500 OE1 GLU A 565 O HOH A 603 2.19 REMARK 500 OD2 ASP B 384 O HOH B 602 2.19 REMARK 500 O HOH A 609 O HOH A 720 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 O HOH B 670 O HOH A 692 3957 2.13 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 TYR C 29 CE1 TYR C 29 CZ -0.083 REMARK 500 SER C 30 CA SER C 30 CB -0.114 REMARK 500 TYR C 32 CE1 TYR C 32 CZ -0.083 REMARK 500 CYS C 96 CB CYS C 96 SG -0.111 REMARK 500 SER C 111 CB SER C 111 OG -0.084 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 TYR C 29 N - CA - C ANGL. DEV. = -26.6 DEGREES REMARK 500 TYR C 29 CA - C - N ANGL. DEV. = 13.7 DEGREES REMARK 500 SER C 30 C - N - CA ANGL. DEV. = 15.3 DEGREES REMARK 500 PRO C 54 C - N - CD ANGL. DEV. = -19.6 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 GLU B 382 122.01 31.65 REMARK 500 ASP B 384 77.31 -100.16 REMARK 500 ASN B 398 40.61 -108.47 REMARK 500 ASN B 406 69.20 37.88 REMARK 500 LEU B 417 6.11 -69.16 REMARK 500 PHE B 423 83.40 -154.25 REMARK 500 SER B 459 -130.16 57.43 REMARK 500 LYS B 502 138.40 -175.57 REMARK 500 SER A 460 130.71 62.23 REMARK 500 ALA A 461 -92.19 -46.45 REMARK 500 ASP A 509 1.25 -68.96 REMARK 500 ASP A 510 12.13 53.67 REMARK 500 THR A 579 -74.10 -98.33 REMARK 500 SER C 30 -58.30 104.97 REMARK 500 PRO C 54 -89.23 46.09 REMARK 500 ASN C 77 28.24 42.17 REMARK 500 ALA C 92 -178.64 -177.60 REMARK 500 GLN D 39 107.83 -163.12 REMARK 500 LEU D 48 -86.01 -118.94 REMARK 500 ASN D 53 50.78 -105.95 REMARK 500 GLU D 55 -25.87 -150.49 REMARK 500 GLU D 89 -9.59 -58.30 REMARK 500 CYS D 105 -72.60 -160.94 REMARK 500 SER D 111 35.87 -147.69 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 C 53 PRO C 54 -114.37 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 B 682 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH B 683 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH B 684 DISTANCE = 6.96 ANGSTROMS DBREF 8IDO B 367 589 UNP R9UQ53 R9UQ53_MERS 367 589 DBREF 8IDO A 367 589 UNP R9UQ53 R9UQ53_MERS 367 589 DBREF 8IDO C 1 135 PDB 8IDO 8IDO 1 135 DBREF 8IDO D 1 135 PDB 8IDO 8IDO 1 135 SEQADV 8IDO HIS B 590 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS B 591 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS B 592 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS B 593 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS B 594 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS B 595 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS A 590 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS A 591 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS A 592 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS A 593 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS A 594 UNP R9UQ53 EXPRESSION TAG SEQADV 8IDO HIS A 595 UNP R9UQ53 EXPRESSION TAG SEQRES 1 B 229 GLU ALA LYS PRO SER GLY SER VAL VAL GLU GLN ALA GLU SEQRES 2 B 229 GLY VAL GLU CYS ASP PHE SER PRO LEU LEU SER GLY THR SEQRES 3 B 229 PRO PRO GLN VAL TYR ASN PHE LYS ARG LEU VAL PHE THR SEQRES 4 B 229 ASN CYS ASN TYR ASN LEU THR LYS LEU LEU SER LEU PHE SEQRES 5 B 229 SER VAL ASN ASP PHE THR CYS SER GLN ILE SER PRO ALA SEQRES 6 B 229 ALA ILE ALA SER ASN CYS TYR SER SER LEU ILE LEU ASP SEQRES 7 B 229 TYR PHE SER TYR PRO LEU SER MET LYS SER ASP LEU SER SEQRES 8 B 229 VAL SER SER ALA GLY PRO ILE SER GLN PHE ASN TYR LYS SEQRES 9 B 229 GLN SER PHE SER ASN PRO THR CYS LEU ILE LEU ALA THR SEQRES 10 B 229 VAL PRO HIS ASN LEU THR THR ILE THR LYS PRO LEU LYS SEQRES 11 B 229 TYR SER TYR ILE ASN LYS CYS SER ARG LEU LEU SER ASP SEQRES 12 B 229 ASP ARG THR GLU VAL PRO GLN LEU VAL ASN ALA ASN GLN SEQRES 13 B 229 TYR SER PRO CYS VAL SER ILE VAL PRO SER THR VAL TRP SEQRES 14 B 229 GLU ASP GLY ASP TYR TYR ARG LYS GLN LEU SER PRO LEU SEQRES 15 B 229 GLU GLY GLY GLY TRP LEU VAL ALA SER GLY SER THR VAL SEQRES 16 B 229 ALA MET THR GLU GLN LEU GLN MET GLY PHE GLY ILE THR SEQRES 17 B 229 VAL GLN TYR GLY THR ASP THR ASN SER VAL CYS PRO LYS SEQRES 18 B 229 LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 A 229 GLU ALA LYS PRO SER GLY SER VAL VAL GLU GLN ALA GLU SEQRES 2 A 229 GLY VAL GLU CYS ASP PHE SER PRO LEU LEU SER GLY THR SEQRES 3 A 229 PRO PRO GLN VAL TYR ASN PHE LYS ARG LEU VAL PHE THR SEQRES 4 A 229 ASN CYS ASN TYR ASN LEU THR LYS LEU LEU SER LEU PHE SEQRES 5 A 229 SER VAL ASN ASP PHE THR CYS SER GLN ILE SER PRO ALA SEQRES 6 A 229 ALA ILE ALA SER ASN CYS TYR SER SER LEU ILE LEU ASP SEQRES 7 A 229 TYR PHE SER TYR PRO LEU SER MET LYS SER ASP LEU SER SEQRES 8 A 229 VAL SER SER ALA GLY PRO ILE SER GLN PHE ASN TYR LYS SEQRES 9 A 229 GLN SER PHE SER ASN PRO THR CYS LEU ILE LEU ALA THR SEQRES 10 A 229 VAL PRO HIS ASN LEU THR THR ILE THR LYS PRO LEU LYS SEQRES 11 A 229 TYR SER TYR ILE ASN LYS CYS SER ARG LEU LEU SER ASP SEQRES 12 A 229 ASP ARG THR GLU VAL PRO GLN LEU VAL ASN ALA ASN GLN SEQRES 13 A 229 TYR SER PRO CYS VAL SER ILE VAL PRO SER THR VAL TRP SEQRES 14 A 229 GLU ASP GLY ASP TYR TYR ARG LYS GLN LEU SER PRO LEU SEQRES 15 A 229 GLU GLY GLY GLY TRP LEU VAL ALA SER GLY SER THR VAL SEQRES 16 A 229 ALA MET THR GLU GLN LEU GLN MET GLY PHE GLY ILE THR SEQRES 17 A 229 VAL GLN TYR GLY THR ASP THR ASN SER VAL CYS PRO LYS SEQRES 18 A 229 LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 135 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 C 135 ALA GLY GLY SER LEU LYS LEU SER CYS SER VAL SER GLY SEQRES 3 C 135 TYR THR TYR SER THR TYR CYS ILE ALA TRP PHE ARG GLN SEQRES 4 C 135 VAL PRO GLY LYS GLU ARG GLU GLY LEU ALA PHE ILE LYS SEQRES 5 C 135 ASN PRO GLU GLY ASN THR ASP TYR ALA ASP SER VAL GLN SEQRES 6 C 135 GLY ARG PHE PHE ILE SER GLN ASP THR VAL ASP ASN THR SEQRES 7 C 135 VAL TYR LEU SER MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 C 135 ALA THR TYR TYR CYS ALA GLY ALA VAL SER ASN TRP VAL SEQRES 9 C 135 CYS GLY MET SER ILE LYS SER GLN GLY TYR GLY MET ASP SEQRES 10 C 135 TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER HIS SEQRES 11 C 135 HIS HIS HIS HIS HIS SEQRES 1 D 135 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 D 135 ALA GLY GLY SER LEU LYS LEU SER CYS SER VAL SER GLY SEQRES 3 D 135 TYR THR TYR SER THR TYR CYS ILE ALA TRP PHE ARG GLN SEQRES 4 D 135 VAL PRO GLY LYS GLU ARG GLU GLY LEU ALA PHE ILE LYS SEQRES 5 D 135 ASN PRO GLU GLY ASN THR ASP TYR ALA ASP SER VAL GLN SEQRES 6 D 135 GLY ARG PHE PHE ILE SER GLN ASP THR VAL ASP ASN THR SEQRES 7 D 135 VAL TYR LEU SER MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 D 135 ALA THR TYR TYR CYS ALA GLY ALA VAL SER ASN TRP VAL SEQRES 9 D 135 CYS GLY MET SER ILE LYS SER GLN GLY TYR GLY MET ASP SEQRES 10 D 135 TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER HIS SEQRES 11 D 135 HIS HIS HIS HIS HIS HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET MAN E 5 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET MAN F 4 11 HET MAN F 5 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 5 NAG 4(C8 H15 N O6) FORMUL 5 BMA 2(C6 H12 O6) FORMUL 5 MAN 4(C6 H12 O6) FORMUL 7 HOH *287(H2 O) HELIX 1 AA1 PHE B 385 SER B 390 5 6 HELIX 2 AA2 GLN B 395 PHE B 399 5 5 HELIX 3 AA3 ASN B 410 LEU B 417 1 8 HELIX 4 AA4 SER B 429 ALA B 434 1 6 HELIX 5 AA5 PRO B 449 MET B 452 5 4 HELIX 6 AA6 LYS B 453 VAL B 458 1 6 HELIX 7 AA7 SER B 459 ALA B 461 5 3 HELIX 8 AA8 GLY B 462 ASN B 468 1 7 HELIX 9 AA9 SER B 524 SER B 528 5 5 HELIX 10 AB1 PHE A 385 SER A 390 1 6 HELIX 11 AB2 GLN A 395 PHE A 399 5 5 HELIX 12 AB3 ASN A 410 LEU A 417 1 8 HELIX 13 AB4 SER A 429 ALA A 434 1 6 HELIX 14 AB5 PRO A 449 SER A 457 5 9 HELIX 15 AB6 GLY A 462 ASN A 468 1 7 HELIX 16 AB7 SER A 524 ILE A 529 5 6 HELIX 17 AB8 LYS C 87 THR C 91 5 5 HELIX 18 AB9 VAL C 104 LYS C 110 1 7 HELIX 19 AC1 LYS D 87 THR D 91 5 5 HELIX 20 AC2 CYS D 105 LYS D 110 1 6 SHEET 1 AA1 5 LYS B 400 PHE B 404 0 SHEET 2 AA1 5 SER B 440 SER B 447 -1 O LEU B 443 N LEU B 402 SHEET 3 AA1 5 GLN B 568 GLN B 576 -1 O GLY B 572 N ASP B 444 SHEET 4 AA1 5 THR B 477 THR B 483 -1 N ALA B 482 O MET B 569 SHEET 5 AA1 5 SER B 419 SER B 426 -1 N SER B 426 O THR B 477 SHEET 1 AA2 2 CYS B 407 TYR B 409 0 SHEET 2 AA2 2 VAL B 584 PRO B 586 1 O CYS B 585 N TYR B 409 SHEET 1 AA3 3 TYR B 497 CYS B 503 0 SHEET 2 AA3 3 ALA B 556 VAL B 561 -1 O SER B 559 N TYR B 499 SHEET 3 AA3 3 TYR B 540 TYR B 541 -1 N TYR B 541 O ALA B 556 SHEET 1 AA4 5 LYS A 400 PHE A 404 0 SHEET 2 AA4 5 SER A 440 SER A 447 -1 O LEU A 443 N LEU A 402 SHEET 3 AA4 5 GLN A 568 GLN A 576 -1 O GLY A 572 N ASP A 444 SHEET 4 AA4 5 THR A 477 THR A 483 -1 N ALA A 482 O MET A 569 SHEET 5 AA4 5 SER A 419 SER A 426 -1 N THR A 424 O LEU A 479 SHEET 1 AA5 2 CYS A 407 TYR A 409 0 SHEET 2 AA5 2 VAL A 584 PRO A 586 1 O CYS A 585 N TYR A 409 SHEET 1 AA6 4 GLU A 513 PRO A 515 0 SHEET 2 AA6 4 TYR A 497 LEU A 506 -1 N ARG A 505 O VAL A 514 SHEET 3 AA6 4 TRP A 553 VAL A 561 -1 O VAL A 555 N SER A 504 SHEET 4 AA6 4 TYR A 540 GLN A 544 -1 N TYR A 541 O ALA A 556 SHEET 1 AA7 4 GLN C 3 SER C 7 0 SHEET 2 AA7 4 LEU C 18 SER C 25 -1 O SER C 25 N GLN C 3 SHEET 3 AA7 4 VAL C 79 MET C 83 -1 O MET C 83 N LEU C 18 SHEET 4 AA7 4 PHE C 69 GLN C 72 -1 N PHE C 69 O SER C 82 SHEET 1 AA8 6 GLY C 10 GLN C 13 0 SHEET 2 AA8 6 THR C 123 SER C 128 1 O THR C 126 N GLY C 10 SHEET 3 AA8 6 ALA C 92 GLY C 98 -1 N TYR C 94 O THR C 123 SHEET 4 AA8 6 CYS C 33 GLN C 39 -1 N PHE C 37 O TYR C 95 SHEET 5 AA8 6 GLU C 46 LYS C 52 -1 O GLU C 46 N ARG C 38 SHEET 6 AA8 6 ASN C 57 TYR C 60 -1 O ASN C 57 N LYS C 52 SHEET 1 AA9 4 GLY C 10 GLN C 13 0 SHEET 2 AA9 4 THR C 123 SER C 128 1 O THR C 126 N GLY C 10 SHEET 3 AA9 4 ALA C 92 GLY C 98 -1 N TYR C 94 O THR C 123 SHEET 4 AA9 4 TYR C 118 TRP C 119 -1 O TYR C 118 N GLY C 98 SHEET 1 AB1 4 GLN D 3 SER D 7 0 SHEET 2 AB1 4 LEU D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AB1 4 VAL D 79 MET D 83 -1 O LEU D 81 N LEU D 20 SHEET 4 AB1 4 PHE D 68 GLN D 72 -1 N SER D 71 O TYR D 80 SHEET 1 AB2 6 GLY D 10 VAL D 12 0 SHEET 2 AB2 6 THR D 123 VAL D 127 1 O THR D 126 N VAL D 12 SHEET 3 AB2 6 ALA D 92 GLY D 98 -1 N TYR D 94 O THR D 123 SHEET 4 AB2 6 CYS D 33 GLN D 39 -1 N ALA D 35 O ALA D 97 SHEET 5 AB2 6 GLU D 46 LYS D 52 -1 O ILE D 51 N ILE D 34 SHEET 6 AB2 6 THR D 58 TYR D 60 -1 O ASP D 59 N PHE D 50 SHEET 1 AB3 4 GLY D 10 VAL D 12 0 SHEET 2 AB3 4 THR D 123 VAL D 127 1 O THR D 126 N VAL D 12 SHEET 3 AB3 4 ALA D 92 GLY D 98 -1 N TYR D 94 O THR D 123 SHEET 4 AB3 4 TYR D 118 TRP D 119 -1 O TYR D 118 N GLY D 98 SSBOND 1 CYS B 383 CYS B 407 1555 1555 2.04 SSBOND 2 CYS B 425 CYS B 478 1555 1555 2.05 SSBOND 3 CYS B 437 CYS B 585 1555 1555 2.03 SSBOND 4 CYS B 503 CYS B 526 1555 1555 2.01 SSBOND 5 CYS A 383 CYS A 407 1555 1555 2.05 SSBOND 6 CYS A 425 CYS A 478 1555 1555 2.05 SSBOND 7 CYS A 437 CYS A 585 1555 1555 2.05 SSBOND 8 CYS A 503 CYS A 526 1555 1555 2.03 SSBOND 9 CYS C 22 CYS C 96 1555 1555 1.99 SSBOND 10 CYS C 33 CYS C 105 1555 1555 2.04 SSBOND 11 CYS D 22 CYS D 96 1555 1555 2.02 SSBOND 12 CYS D 33 CYS D 105 1555 1555 2.03 LINK ND2 ASN B 410 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN A 410 C1 NAG F 1 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.37 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.38 LINK O3 BMA E 3 C1 MAN E 4 1555 1555 1.38 LINK O6 BMA E 3 C1 MAN E 5 1555 1555 1.38 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.37 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.38 LINK O3 BMA F 3 C1 MAN F 4 1555 1555 1.37 LINK O6 BMA F 3 C1 MAN F 5 1555 1555 1.38 CISPEP 1 TYR C 29 SER C 30 0 7.70 CRYST1 175.896 47.190 124.213 90.00 90.00 90.00 P 21 21 2 8 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 0.005685 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008051 0.00000