HEADER IMMUNE SYSTEM/HYDROLASE 25-JAN-19 6JB8 TITLE CRYSTAL STRUCTURE OF NANOBODY D3-L11 IN COMPLEX WITH HEN EGG-WHITE TITLE 2 LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY D3-L11; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LYSOZYME C; COMPND 7 CHAIN: B; COMPND 8 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELUS DROMEDARIUS; SOURCE 3 ORGANISM_TAXID: 9838; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 8 ORGANISM_COMMON: CHICKEN; SOURCE 9 ORGANISM_TAXID: 9031 KEYWDS NANOBODY, HOT-SPOT MUTAGENESIS, THERMODYNAMICS, BIOMOLECULAR KEYWDS 2 RECOGNITION, IMMUNE SYSTEM, IMMUNE SYSTEM-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,H.TAMURA,H.AKIBA,K.TSUMOTO REVDAT 3 22-NOV-23 6JB8 1 LINK REVDAT 2 13-NOV-19 6JB8 1 JRNL REVDAT 1 06-NOV-19 6JB8 0 JRNL AUTH H.AKIBA,H.TAMURA,M.KIYOSHI,S.YANAKA,K.SUGASE,J.M.M.CAAVEIRO, JRNL AUTH 2 K.TSUMOTO JRNL TITL STRUCTURAL AND THERMODYNAMIC BASIS FOR THE RECOGNITION OF JRNL TITL 2 THE SUBSTRATE-BINDING CLEFT ON HEN EGG LYSOZYME BY A JRNL TITL 3 SINGLE-DOMAIN ANTIBODY. JRNL REF SCI REP V. 9 15481 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 31664051 JRNL DOI 10.1038/S41598-019-50722-Y REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 25271 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1107 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1216 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : -0.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.409 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2057 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1822 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2792 ; 1.815 ; 1.923 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4224 ; 1.095 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 6.763 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;36.954 ;23.263 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 336 ;14.069 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.300 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 298 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2355 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 459 ; 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): 1033 ; 1.097 ; 1.849 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1032 ; 1.097 ; 1.847 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1293 ; 1.567 ; 2.766 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1294 ; 1.567 ; 2.768 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1024 ; 1.432 ; 2.028 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1021 ; 1.420 ; 2.023 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1490 ; 2.165 ; 2.974 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2445 ; 4.518 ;23.036 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2371 ; 4.399 ;22.101 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 2 A 126 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8634 -24.4123 7.0154 REMARK 3 T TENSOR REMARK 3 T11: 0.0627 T22: 0.0487 REMARK 3 T33: 0.0712 T12: 0.0092 REMARK 3 T13: 0.0185 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 2.0421 L22: 3.2890 REMARK 3 L33: 1.2420 L12: 0.7086 REMARK 3 L13: -0.1265 L23: 0.8203 REMARK 3 S TENSOR REMARK 3 S11: -0.0827 S12: -0.0347 S13: -0.3398 REMARK 3 S21: 0.0482 S22: 0.0943 S23: -0.2606 REMARK 3 S31: 0.2530 S32: 0.0432 S33: -0.0116 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 129 REMARK 3 ORIGIN FOR THE GROUP (A): 6.7656 1.4969 21.3919 REMARK 3 T TENSOR REMARK 3 T11: 0.0507 T22: 0.0323 REMARK 3 T33: 0.0110 T12: 0.0031 REMARK 3 T13: -0.0102 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.9851 L22: 1.3446 REMARK 3 L33: 1.9801 L12: 0.1697 REMARK 3 L13: -0.4036 L23: 0.4214 REMARK 3 S TENSOR REMARK 3 S11: -0.0410 S12: -0.1587 S13: 0.0782 REMARK 3 S21: 0.0898 S22: 0.0539 S23: -0.0880 REMARK 3 S31: -0.1265 S32: 0.1037 S33: -0.0129 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 6JB8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300010790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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-NW12A 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.1.0 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26392 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 6JB2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS-HCL, 100MM NACL, 100MM REMARK 280 NANO3, 16% PEG 3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.74000 REMARK 290 SMTRY3 2 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: 2320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 ASP A 1 REMARK 465 SER A 127 REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 GLY A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 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 OD2 ASP A 84 O HOH A 301 1.90 REMARK 500 O HOH A 317 O HOH A 367 2.17 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 A 32 -78.86 -94.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 27 O REMARK 620 2 SER A 27 OG 75.3 REMARK 620 3 SER A 30 OG 149.9 120.6 REMARK 620 4 HOH A 363 O 75.3 115.6 113.3 REMARK 620 5 HOH A 406 O 119.9 98.0 85.0 53.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 57 O REMARK 620 2 GOL B 201 O1 93.7 REMARK 620 3 HOH B 341 O 163.5 85.7 REMARK 620 4 HOH B 349 O 82.2 82.8 114.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 60 O REMARK 620 2 CYS B 64 O 82.8 REMARK 620 3 SER B 72 OG 89.8 161.7 REMARK 620 4 ARG B 73 O 98.6 95.6 102.0 REMARK 620 5 HOH B 381 O 167.9 99.9 84.1 92.9 REMARK 620 6 HOH B 390 O 84.6 87.1 75.6 176.0 83.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 205 DBREF 6JB8 A 1 136 PDB 6JB8 6JB8 1 136 DBREF 6JB8 B 1 129 UNP P00698 LYSC_CHICK 19 147 SEQRES 1 A 136 ASP VAL GLN LEU VAL GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 A 136 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 136 SER THR ASP SER ILE GLU TYR MET THR TRP PHE ARG GLN SEQRES 4 A 136 ALA PRO GLY LYS ALA ARG GLU GLY VAL ALA ALA LEU TYR SEQRES 5 A 136 THR HIS THR GLY ASN THR TYR TYR THR ASP SER VAL LYS SEQRES 6 A 136 GLY ARG PHE THR ILE SER GLN ASP LYS ALA LYS ASN MET SEQRES 7 A 136 ALA TYR LEU ARG MET ASP SER VAL LYS SER GLU ASP THR SEQRES 8 A 136 ALA ILE TYR THR CYS GLY ALA THR ARG LYS TYR VAL PRO SEQRES 9 A 136 VAL ARG PHE ALA LEU ASP GLN SER SER TYR ASP TYR TRP SEQRES 10 A 136 GLY GLN GLY THR GLN VAL THR VAL SER SER SER ALA GLY SEQRES 11 A 136 HIS HIS HIS HIS HIS HIS SEQRES 1 B 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 B 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 B 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 B 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 B 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 B 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 B 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 B 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 B 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 B 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU HET NO3 A 201 4 HET NA A 202 1 HET GOL B 201 6 HET GOL B 202 6 HET NA B 203 1 HET NA B 204 1 HET CL B 205 1 HETNAM NO3 NITRATE ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NO3 N O3 1- FORMUL 4 NA 3(NA 1+) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 9 CL CL 1- FORMUL 10 HOH *276(H2 O) HELIX 1 AA1 SER A 27 ILE A 31 5 5 HELIX 2 AA2 ASP A 62 LYS A 65 5 4 HELIX 3 AA3 LYS A 74 LYS A 76 5 3 HELIX 4 AA4 LYS A 87 THR A 91 5 5 HELIX 5 AA5 PRO A 104 ALA A 108 5 5 HELIX 6 AA6 ASP A 110 TYR A 114 5 5 HELIX 7 AA7 GLY B 4 HIS B 15 1 12 HELIX 8 AA8 ASN B 19 TYR B 23 5 5 HELIX 9 AA9 SER B 24 ASN B 37 1 14 HELIX 10 AB1 PRO B 79 SER B 85 5 7 HELIX 11 AB2 ILE B 88 SER B 100 1 13 HELIX 12 AB3 ASN B 103 ALA B 107 5 5 HELIX 13 AB4 TRP B 108 CYS B 115 1 8 HELIX 14 AB5 ASP B 119 ARG B 125 5 7 SHEET 1 AA1 4 LEU A 4 GLY A 8 0 SHEET 2 AA1 4 LEU A 18 ALA A 24 -1 O ALA A 23 N VAL A 5 SHEET 3 AA1 4 MET A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N SER A 71 O TYR A 80 SHEET 1 AA2 6 GLY A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 121 VAL A 125 1 O GLN A 122 N GLY A 10 SHEET 3 AA2 6 ALA A 92 ALA A 98 -1 N TYR A 94 O THR A 121 SHEET 4 AA2 6 TYR A 33 GLN A 39 -1 N THR A 35 O GLY A 97 SHEET 5 AA2 6 GLU A 46 TYR A 52 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 THR A 58 TYR A 60 -1 O TYR A 59 N ALA A 50 SHEET 1 AA3 4 GLY A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 121 VAL A 125 1 O GLN A 122 N GLY A 10 SHEET 3 AA3 4 ALA A 92 ALA A 98 -1 N TYR A 94 O THR A 121 SHEET 4 AA3 4 TYR A 116 TRP A 117 -1 O TYR A 116 N ALA A 98 SHEET 1 AA4 3 THR B 43 ARG B 45 0 SHEET 2 AA4 3 THR B 51 TYR B 53 -1 O ASP B 52 N ASN B 44 SHEET 3 AA4 3 ILE B 58 ASN B 59 -1 O ILE B 58 N TYR B 53 SSBOND 1 CYS B 6 CYS B 127 1555 1555 2.04 SSBOND 2 CYS B 30 CYS B 115 1555 1555 2.04 SSBOND 3 CYS B 64 CYS B 80 1555 1555 2.02 SSBOND 4 CYS B 76 CYS B 94 1555 1555 2.05 LINK O SER A 27 NA NA A 202 1555 1555 2.25 LINK OG SER A 27 NA NA A 202 1555 1555 2.55 LINK OG SER A 30 NA NA A 202 1555 1555 2.30 LINK NA NA A 202 O HOH A 363 1555 1555 2.37 LINK NA NA A 202 O HOH A 406 1555 1555 3.17 LINK O GLN B 57 NA NA B 204 1555 1555 2.49 LINK O SER B 60 NA NA B 203 1555 1555 2.41 LINK O CYS B 64 NA NA B 203 1555 1555 2.38 LINK OG SER B 72 NA NA B 203 1555 1555 2.54 LINK O ARG B 73 NA NA B 203 1555 1555 2.37 LINK O1 GOL B 201 NA NA B 204 1555 1555 2.47 LINK NA NA B 203 O HOH B 381 1555 1555 2.26 LINK NA NA B 203 O HOH B 390 1555 1555 2.52 LINK NA NA B 204 O HOH B 341 1555 1555 2.20 LINK NA NA B 204 O HOH B 349 1555 1555 2.34 SITE 1 AC1 4 SER A 27 THR A 28 ASP A 29 HOH A 339 SITE 1 AC2 3 SER A 27 SER A 30 HOH A 363 SITE 1 AC3 10 TYR A 102 GLN B 57 ILE B 58 ASN B 59 SITE 2 AC3 10 TRP B 63 ALA B 107 TRP B 108 NA B 204 SITE 3 AC3 10 HOH B 343 HOH B 349 SITE 1 AC4 2 TYR B 20 ARG B 21 SITE 1 AC5 6 SER B 60 CYS B 64 SER B 72 ARG B 73 SITE 2 AC5 6 HOH B 381 HOH B 390 SITE 1 AC6 5 GLU B 35 GLN B 57 GOL B 201 HOH B 341 SITE 2 AC6 5 HOH B 349 SITE 1 AC7 3 GLN A 3 ILE B 88 HOH B 432 CRYST1 40.240 49.480 59.280 90.00 93.40 90.00 P 1 21 1 2 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 0.024851 0.000000 0.001476 0.00000 SCALE2 0.000000 0.020210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016899 0.00000