HEADER MEMBRANE PROTEIN 27-JUN-23 8JUR TITLE CRYSTAL STRUCTURE OF CHITOPORIN FROM VIBRIO HARVEYI IN COMPLEX WITH TITLE 2 GENTAMICIN C1A (MULTIPLE BINDING SITES) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITOPORIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO HARVEYI; SOURCE 3 ORGANISM_TAXID: 669; SOURCE 4 GENE: CHIP, AL538_13355, VCHENC02_0932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OUTER-MEMBRANE PROTEIN, SUGAR-SPECIFIC PORIN, MARINE BACTERIA, KEYWDS 2 CHITOOLIGOSACHARIDE, PORIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SANRAM,W.SUGINTA,R.ROBINSON REVDAT 1 03-JUL-24 8JUR 0 JRNL AUTH S.SANRAM,W.SUGINTA JRNL TITL CRYSTAL STRUCTURE OF CHITOPORIN FROM VIBRIO HARVEYI IN JRNL TITL 2 COMPLEX WITH GENTAMICIN C1A (MULTIPLE BINDING SITES) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 2.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 37137 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1869 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 20.1600 - 6.7800 1.00 2882 157 0.2120 0.2679 REMARK 3 2 6.7800 - 5.4200 1.00 2788 145 0.2024 0.2322 REMARK 3 3 5.4100 - 4.7400 1.00 2775 148 0.1792 0.2434 REMARK 3 4 4.7400 - 4.3100 1.00 2753 108 0.1814 0.2174 REMARK 3 5 4.3100 - 4.0100 1.00 2742 151 0.2028 0.2585 REMARK 3 6 4.0100 - 3.7700 1.00 2716 148 0.1936 0.3056 REMARK 3 7 3.7700 - 3.5800 1.00 2723 135 0.1931 0.2473 REMARK 3 8 3.5800 - 3.4300 1.00 2713 129 0.1869 0.2746 REMARK 3 9 3.4300 - 3.3000 1.00 2728 139 0.1982 0.2658 REMARK 3 10 3.3000 - 3.1800 1.00 2660 157 0.2200 0.2934 REMARK 3 11 3.1800 - 3.0800 1.00 2686 144 0.2322 0.3087 REMARK 3 12 3.0800 - 3.0000 0.99 2647 167 0.2549 0.3001 REMARK 3 13 3.0000 - 2.9200 0.92 2455 141 0.2760 0.3468 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.010 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 8382 REMARK 3 ANGLE : 0.976 11359 REMARK 3 CHIRALITY : 0.060 1107 REMARK 3 PLANARITY : 0.007 1527 REMARK 3 DIHEDRAL : 9.169 1231 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): -20.3382 -21.9950 32.9931 REMARK 3 T TENSOR REMARK 3 T11: 0.0705 T22: 0.1322 REMARK 3 T33: 0.1473 T12: 0.0153 REMARK 3 T13: 0.0033 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.1228 L22: 0.2537 REMARK 3 L33: 0.6849 L12: 0.0600 REMARK 3 L13: 0.1582 L23: 0.1689 REMARK 3 S TENSOR REMARK 3 S11: 0.0178 S12: -0.0012 S13: -0.0140 REMARK 3 S21: 0.0711 S22: 0.0141 S23: -0.0312 REMARK 3 S31: 0.0047 S32: -0.0495 S33: 0.0010 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 8JUR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : LN2-COOLED, FIXED-EXIT DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : LN2-COOLED FIXED-EXIT DOUBLE REMARK 200 CRYSTAL SI(111) MONOCHROMATOR , REMARK 200 A PAIR OF K-B FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37198 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 1.12100 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: PHENIX REMARK 200 STARTING MODEL: 5MDQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: KITS: MEMTRANS(A6) 0.08 M SODIUM REMARK 280 CHLORIDE, 0.025 M LITHIUM SULFATE, 0.05 M HEPES PH 8.2, AND 27% REMARK 280 V/V PEG 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 43.16300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.89350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 67.05150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.89350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.16300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 67.05150 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: 16340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -166.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 14 CG CD CE NZ REMARK 470 MET A 159 CG SD CE REMARK 470 LYS A 193 CG CD CE NZ REMARK 470 LEU A 194 CG CD1 CD2 REMARK 470 GLU A 210 CG CD OE1 OE2 REMARK 470 GLU A 281 CG CD OE1 OE2 REMARK 470 LYS A 285 CG CD CE NZ REMARK 470 GLU A 320 CG CD OE1 OE2 REMARK 470 ASP A 327 CG OD1 OD2 REMARK 470 GLU B 10 CG CD OE1 OE2 REMARK 470 LYS B 40 CG CD CE NZ REMARK 470 MET B 159 CG SD CE REMARK 470 ASP B 162 CG OD1 OD2 REMARK 470 LYS B 193 CG CD CE NZ REMARK 470 LEU B 194 CG CD1 CD2 REMARK 470 GLU B 230 CG CD OE1 OE2 REMARK 470 ASN B 231 CG OD1 ND2 REMARK 470 LYS B 285 CG CD CE NZ REMARK 470 ASP B 293 CG OD1 OD2 REMARK 470 LYS C 163 CG CD CE NZ REMARK 470 LEU C 194 CG CD1 CD2 REMARK 470 SER C 288 OG 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 SER A 5 -152.35 55.32 REMARK 500 SER A 18 53.25 -109.10 REMARK 500 ASP A 81 66.33 -158.89 REMARK 500 ARG A 94 -153.90 -101.10 REMARK 500 ASP A 135 -89.27 -75.78 REMARK 500 TYR A 145 171.17 177.35 REMARK 500 ASP A 147 -110.60 -98.47 REMARK 500 ALA A 161 19.29 56.08 REMARK 500 LYS A 163 -32.47 -135.95 REMARK 500 ASP A 327 36.06 74.74 REMARK 500 ASN B 4 27.81 -142.34 REMARK 500 SER B 5 -148.51 51.92 REMARK 500 SER B 18 61.42 -112.14 REMARK 500 ASP B 81 62.95 -158.08 REMARK 500 ARG B 94 -155.60 -101.58 REMARK 500 ALA B 125 -170.36 -66.50 REMARK 500 SER B 126 -17.50 59.64 REMARK 500 ASP B 135 -85.50 -76.74 REMARK 500 TYR B 145 171.95 179.65 REMARK 500 ASP B 147 -114.72 -91.69 REMARK 500 ALA B 161 19.27 54.77 REMARK 500 LYS B 163 -30.60 -135.83 REMARK 500 ASP B 327 36.49 71.34 REMARK 500 ASN C 4 21.29 -144.85 REMARK 500 SER C 5 -143.92 46.81 REMARK 500 SER C 18 55.01 -114.37 REMARK 500 ASP C 81 65.31 -160.92 REMARK 500 ARG C 94 -159.98 -100.92 REMARK 500 SER C 126 -14.31 66.06 REMARK 500 ASP C 135 -83.01 -75.73 REMARK 500 TYR C 145 171.94 179.19 REMARK 500 ASP C 147 -115.94 -95.42 REMARK 500 ALA C 161 18.27 53.79 REMARK 500 LYS C 163 -35.21 -131.51 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 503 DISTANCE = 6.79 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 C8E C 401 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 O REMARK 620 2 ASN A 44 O 75.4 REMARK 620 3 GLY A 46 O 68.8 86.7 REMARK 620 4 GLY C 181 O 87.5 85.1 156.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 107 OE1 REMARK 620 2 ARG A 154 O 170.2 REMARK 620 3 ASP A 156 OD2 72.6 115.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 146 OE1 REMARK 620 2 GLN A 149 OE1 90.0 REMARK 620 3 ASP A 174 OD1 80.2 62.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 44 O REMARK 620 2 GLY B 46 O 71.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO B 82 O REMARK 620 2 GLY B 85 O 62.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 181 O REMARK 620 2 ASP C 43 O 82.0 REMARK 620 3 ASN C 44 O 75.1 69.7 REMARK 620 4 GLY C 46 O 151.9 70.9 88.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN C 146 OE1 REMARK 620 2 GLN C 149 OE1 63.9 REMARK 620 3 ASP C 174 OD1 76.0 70.0 REMARK 620 4 ASP C 174 OD2 79.3 108.7 41.9 REMARK 620 N 1 2 3 DBREF1 8JUR A 1 350 UNP A0A454DK07_VIBHA DBREF2 8JUR A A0A454DK07 25 374 DBREF1 8JUR B 1 350 UNP A0A454DK07_VIBHA DBREF2 8JUR B A0A454DK07 25 374 DBREF1 8JUR C 1 350 UNP A0A454DK07_VIBHA DBREF2 8JUR C A0A454DK07 25 374 SEQRES 1 A 350 ASP GLY ALA ASN SER ASP ALA ALA LYS GLU TYR LEU THR SEQRES 2 A 350 LYS ASP SER PHE SER TYR GLU VAL TYR GLY ILE ILE ALA SEQRES 3 A 350 MET GLN ALA ALA TYR ARG ASP TYR ASP SER GLY ASP ALA SEQRES 4 A 350 LYS GLN ASP ASP ASN LEU GLY GLY MET GLN LEU ASN ASN SEQRES 5 A 350 GLU SER ARG ILE GLY PHE ARG GLY LYS LYS GLN PHE ALA SEQRES 6 A 350 ASN PHE GLU PRO THR PHE ILE TRP GLN ILE GLU GLY GLY SEQRES 7 A 350 TYR VAL ASP PRO SER PHE GLY GLY GLU GLY ALA GLY LEU SEQRES 8 A 350 GLY GLU ARG ASP THR PHE VAL GLY PHE GLU SER ALA SER SEQRES 9 A 350 TRP GLY GLN VAL ARG LEU GLY ARG VAL LEU THR PRO MET SEQRES 10 A 350 TYR GLU LEU VAL ASP TRP PRO ALA SER ASN PRO GLY LEU SEQRES 11 A 350 GLY ASP VAL TYR ASP TRP GLY GLY ALA ILE GLY GLY ALA SEQRES 12 A 350 LYS TYR GLN ASP ARG GLN SER ASN THR ILE ARG TRP ASP SEQRES 13 A 350 SER PRO MET TYR ALA ASP LYS PHE SER ILE ASP ALA ALA SEQRES 14 A 350 VAL GLY ALA GLY ASP LYS ALA GLY LEU GLY ALA GLY ASP SEQRES 15 A 350 ASP TYR TRP GLY GLY ILE ALA ALA HIS TYR LYS LEU GLY SEQRES 16 A 350 PRO LEU GLN LEU ASP ALA ALA TYR GLU GLY ASN ARG ASN SEQRES 17 A 350 ILE GLU ALA GLU GLY GLN THR TRP GLU ASN ASN THR TYR SEQRES 18 A 350 LEU VAL GLY VAL GLN GLY TRP PHE GLU ASN GLY ILE SER SEQRES 19 A 350 PHE PHE ALA GLN TYR LYS TYR MET GLU ALA ASP ALA SER SEQRES 20 A 350 ASN GLY VAL ASN GLU LYS GLN ASP ALA MET SER ALA GLY SEQRES 21 A 350 LEU MET TYR THR THR GLY ASP TRP GLN TYR LYS LEU GLY SEQRES 22 A 350 TYR ALA ALA ASN PHE ASP LEU GLU ARG ASP GLY LYS THR SEQRES 23 A 350 LEU SER ASN THR SER ASP ASP VAL VAL SER ALA GLN ILE SEQRES 24 A 350 MET TYR PHE VAL ASP PRO SER ALA VAL LEU TYR ALA ARG SEQRES 25 A 350 ALA ARG MET ASN ASP PHE ASN GLU GLY LEU ASP GLY LEU SEQRES 26 A 350 ASP ASP ALA ALA ARG TRP THR SER GLY THR ASN GLY ASP SEQRES 27 A 350 TYR ASN GLU TYR SER VAL GLY VAL GLU TYR TYR PHE SEQRES 1 B 350 ASP GLY ALA ASN SER ASP ALA ALA LYS GLU TYR LEU THR SEQRES 2 B 350 LYS ASP SER PHE SER TYR GLU VAL TYR GLY ILE ILE ALA SEQRES 3 B 350 MET GLN ALA ALA TYR ARG ASP TYR ASP SER GLY ASP ALA SEQRES 4 B 350 LYS GLN ASP ASP ASN LEU GLY GLY MET GLN LEU ASN ASN SEQRES 5 B 350 GLU SER ARG ILE GLY PHE ARG GLY LYS LYS GLN PHE ALA SEQRES 6 B 350 ASN PHE GLU PRO THR PHE ILE TRP GLN ILE GLU GLY GLY SEQRES 7 B 350 TYR VAL ASP PRO SER PHE GLY GLY GLU GLY ALA GLY LEU SEQRES 8 B 350 GLY GLU ARG ASP THR PHE VAL GLY PHE GLU SER ALA SER SEQRES 9 B 350 TRP GLY GLN VAL ARG LEU GLY ARG VAL LEU THR PRO MET SEQRES 10 B 350 TYR GLU LEU VAL ASP TRP PRO ALA SER ASN PRO GLY LEU SEQRES 11 B 350 GLY ASP VAL TYR ASP TRP GLY GLY ALA ILE GLY GLY ALA SEQRES 12 B 350 LYS TYR GLN ASP ARG GLN SER ASN THR ILE ARG TRP ASP SEQRES 13 B 350 SER PRO MET TYR ALA ASP LYS PHE SER ILE ASP ALA ALA SEQRES 14 B 350 VAL GLY ALA GLY ASP LYS ALA GLY LEU GLY ALA GLY ASP SEQRES 15 B 350 ASP TYR TRP GLY GLY ILE ALA ALA HIS TYR LYS LEU GLY SEQRES 16 B 350 PRO LEU GLN LEU ASP ALA ALA TYR GLU GLY ASN ARG ASN SEQRES 17 B 350 ILE GLU ALA GLU GLY GLN THR TRP GLU ASN ASN THR TYR SEQRES 18 B 350 LEU VAL GLY VAL GLN GLY TRP PHE GLU ASN GLY ILE SER SEQRES 19 B 350 PHE PHE ALA GLN TYR LYS TYR MET GLU ALA ASP ALA SER SEQRES 20 B 350 ASN GLY VAL ASN GLU LYS GLN ASP ALA MET SER ALA GLY SEQRES 21 B 350 LEU MET TYR THR THR GLY ASP TRP GLN TYR LYS LEU GLY SEQRES 22 B 350 TYR ALA ALA ASN PHE ASP LEU GLU ARG ASP GLY LYS THR SEQRES 23 B 350 LEU SER ASN THR SER ASP ASP VAL VAL SER ALA GLN ILE SEQRES 24 B 350 MET TYR PHE VAL ASP PRO SER ALA VAL LEU TYR ALA ARG SEQRES 25 B 350 ALA ARG MET ASN ASP PHE ASN GLU GLY LEU ASP GLY LEU SEQRES 26 B 350 ASP ASP ALA ALA ARG TRP THR SER GLY THR ASN GLY ASP SEQRES 27 B 350 TYR ASN GLU TYR SER VAL GLY VAL GLU TYR TYR PHE SEQRES 1 C 350 ASP GLY ALA ASN SER ASP ALA ALA LYS GLU TYR LEU THR SEQRES 2 C 350 LYS ASP SER PHE SER TYR GLU VAL TYR GLY ILE ILE ALA SEQRES 3 C 350 MET GLN ALA ALA TYR ARG ASP TYR ASP SER GLY ASP ALA SEQRES 4 C 350 LYS GLN ASP ASP ASN LEU GLY GLY MET GLN LEU ASN ASN SEQRES 5 C 350 GLU SER ARG ILE GLY PHE ARG GLY LYS LYS GLN PHE ALA SEQRES 6 C 350 ASN PHE GLU PRO THR PHE ILE TRP GLN ILE GLU GLY GLY SEQRES 7 C 350 TYR VAL ASP PRO SER PHE GLY GLY GLU GLY ALA GLY LEU SEQRES 8 C 350 GLY GLU ARG ASP THR PHE VAL GLY PHE GLU SER ALA SER SEQRES 9 C 350 TRP GLY GLN VAL ARG LEU GLY ARG VAL LEU THR PRO MET SEQRES 10 C 350 TYR GLU LEU VAL ASP TRP PRO ALA SER ASN PRO GLY LEU SEQRES 11 C 350 GLY ASP VAL TYR ASP TRP GLY GLY ALA ILE GLY GLY ALA SEQRES 12 C 350 LYS TYR GLN ASP ARG GLN SER ASN THR ILE ARG TRP ASP SEQRES 13 C 350 SER PRO MET TYR ALA ASP LYS PHE SER ILE ASP ALA ALA SEQRES 14 C 350 VAL GLY ALA GLY ASP LYS ALA GLY LEU GLY ALA GLY ASP SEQRES 15 C 350 ASP TYR TRP GLY GLY ILE ALA ALA HIS TYR LYS LEU GLY SEQRES 16 C 350 PRO LEU GLN LEU ASP ALA ALA TYR GLU GLY ASN ARG ASN SEQRES 17 C 350 ILE GLU ALA GLU GLY GLN THR TRP GLU ASN ASN THR TYR SEQRES 18 C 350 LEU VAL GLY VAL GLN GLY TRP PHE GLU ASN GLY ILE SER SEQRES 19 C 350 PHE PHE ALA GLN TYR LYS TYR MET GLU ALA ASP ALA SER SEQRES 20 C 350 ASN GLY VAL ASN GLU LYS GLN ASP ALA MET SER ALA GLY SEQRES 21 C 350 LEU MET TYR THR THR GLY ASP TRP GLN TYR LYS LEU GLY SEQRES 22 C 350 TYR ALA ALA ASN PHE ASP LEU GLU ARG ASP GLY LYS THR SEQRES 23 C 350 LEU SER ASN THR SER ASP ASP VAL VAL SER ALA GLN ILE SEQRES 24 C 350 MET TYR PHE VAL ASP PRO SER ALA VAL LEU TYR ALA ARG SEQRES 25 C 350 ALA ARG MET ASN ASP PHE ASN GLU GLY LEU ASP GLY LEU SEQRES 26 C 350 ASP ASP ALA ALA ARG TRP THR SER GLY THR ASN GLY ASP SEQRES 27 C 350 TYR ASN GLU TYR SER VAL GLY VAL GLU TYR TYR PHE HET C8E A 401 21 HET NA A 402 1 HET NA A 403 1 HET NA A 404 1 HET LLL A 405 31 HET C8E B 401 21 HET NA B 402 1 HET NA B 403 1 HET NA B 404 1 HET C8E C 401 10 HET NA C 402 1 HET NA C 403 1 HETNAM C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE HETNAM NA SODIUM ION HETNAM LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R, HETNAM 2 LLL 3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2- HETNAM 3 LLL YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4- HETNAM 4 LLL (METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL HETSYN LLL GENTAMICIN C1A FORMUL 4 C8E 3(C16 H34 O5) FORMUL 5 NA 8(NA 1+) FORMUL 8 LLL C19 H39 N5 O7 FORMUL 16 HOH *14(H2 O) HELIX 1 AA1 ASP A 6 LEU A 12 1 7 HELIX 2 AA2 ASP A 38 GLY A 46 1 9 HELIX 3 AA3 THR A 115 TRP A 123 1 9 HELIX 4 AA4 LEU A 130 ASP A 135 1 6 HELIX 5 AA5 MET A 159 ASP A 162 5 4 HELIX 6 AA6 LYS A 175 GLY A 179 5 5 HELIX 7 AA7 ASP B 6 LEU B 12 1 7 HELIX 8 AA8 ASP B 38 GLY B 46 1 9 HELIX 9 AA9 THR B 115 TRP B 123 1 9 HELIX 10 AB1 LEU B 130 ASP B 135 1 6 HELIX 11 AB2 MET B 159 ASP B 162 5 4 HELIX 12 AB3 LYS B 175 GLY B 179 5 5 HELIX 13 AB4 ASP C 6 LEU C 12 1 7 HELIX 14 AB5 ASP C 38 GLY C 46 1 9 HELIX 15 AB6 THR C 115 TRP C 123 1 9 HELIX 16 AB7 LEU C 130 ASP C 135 1 6 HELIX 17 AB8 MET C 159 ASP C 162 5 4 HELIX 18 AB9 LYS C 175 GLY C 179 5 5 SHEET 1 AA115 GLY A 47 ASN A 52 0 SHEET 2 AA115 GLU A 20 ASP A 35 -1 N GLN A 28 O ASN A 51 SHEET 3 AA115 ARG A 55 LYS A 62 -1 O GLY A 57 N TYR A 22 SHEET 4 AA115 THR A 70 GLU A 76 -1 O PHE A 71 N LYS A 62 SHEET 5 AA115 THR A 96 SER A 102 -1 O GLY A 99 N ILE A 72 SHEET 6 AA115 GLY A 106 LEU A 114 -1 O ARG A 112 N THR A 96 SHEET 7 AA115 ARG A 148 ASP A 156 -1 O ASP A 156 N GLN A 107 SHEET 8 AA115 PHE A 164 ALA A 172 -1 O ALA A 168 N TRP A 155 SHEET 9 AA115 TYR A 184 LEU A 194 -1 O GLY A 187 N ALA A 169 SHEET 10 AA115 LEU A 197 ALA A 211 -1 O ALA A 201 N ALA A 190 SHEET 11 AA115 GLN A 214 TRP A 228 -1 O ASN A 218 N ASN A 206 SHEET 12 AA115 ILE A 233 ALA A 246 -1 O TYR A 239 N VAL A 223 SHEET 13 AA115 ASN A 251 THR A 265 -1 O ALA A 256 N LYS A 240 SHEET 14 AA115 GLU A 281 ARG A 282 -1 O GLU A 281 N LYS A 253 SHEET 15 AA115 LYS A 285 THR A 286 -1 O LYS A 285 N ARG A 282 SHEET 1 AA2 9 GLY A 47 ASN A 52 0 SHEET 2 AA2 9 GLU A 20 ASP A 35 -1 N GLN A 28 O ASN A 51 SHEET 3 AA2 9 ASP A 338 TYR A 349 -1 O ASP A 338 N ASP A 35 SHEET 4 AA2 9 ALA A 307 ASP A 317 -1 N ARG A 312 O SER A 343 SHEET 5 AA2 9 ASP A 292 ASP A 304 -1 N TYR A 301 O LEU A 309 SHEET 6 AA2 9 TRP A 268 ASN A 277 -1 N GLY A 273 O SER A 296 SHEET 7 AA2 9 ASN A 251 THR A 265 -1 N THR A 265 O TRP A 268 SHEET 8 AA2 9 GLU A 281 ARG A 282 -1 O GLU A 281 N LYS A 253 SHEET 9 AA2 9 LYS A 285 THR A 286 -1 O LYS A 285 N ARG A 282 SHEET 1 AA315 GLY B 47 ASN B 52 0 SHEET 2 AA315 GLU B 20 ASP B 35 -1 N GLN B 28 O ASN B 51 SHEET 3 AA315 ARG B 55 LYS B 62 -1 O GLY B 57 N TYR B 22 SHEET 4 AA315 THR B 70 GLU B 76 -1 O ILE B 75 N PHE B 58 SHEET 5 AA315 THR B 96 SER B 102 -1 O GLY B 99 N ILE B 72 SHEET 6 AA315 GLY B 106 LEU B 114 -1 O ARG B 112 N THR B 96 SHEET 7 AA315 ARG B 148 ASP B 156 -1 O ASP B 156 N GLN B 107 SHEET 8 AA315 PHE B 164 ALA B 172 -1 O ALA B 168 N TRP B 155 SHEET 9 AA315 TYR B 184 LEU B 194 -1 O ALA B 189 N ASP B 167 SHEET 10 AA315 LEU B 197 ALA B 211 -1 O LEU B 199 N TYR B 192 SHEET 11 AA315 GLN B 214 TRP B 228 -1 O GLY B 224 N ASP B 200 SHEET 12 AA315 ILE B 233 ALA B 246 -1 O GLU B 243 N ASN B 219 SHEET 13 AA315 ASN B 251 THR B 265 -1 O ALA B 256 N LYS B 240 SHEET 14 AA315 LEU B 280 ARG B 282 -1 O GLU B 281 N LYS B 253 SHEET 15 AA315 LYS B 285 LEU B 287 -1 O LEU B 287 N LEU B 280 SHEET 1 AA4 9 GLY B 47 ASN B 52 0 SHEET 2 AA4 9 GLU B 20 ASP B 35 -1 N GLN B 28 O ASN B 51 SHEET 3 AA4 9 ASP B 338 TYR B 349 -1 O TYR B 342 N TYR B 31 SHEET 4 AA4 9 ALA B 307 ASP B 317 -1 N ARG B 312 O SER B 343 SHEET 5 AA4 9 ASP B 292 ASP B 304 -1 N ASP B 293 O ASP B 317 SHEET 6 AA4 9 TRP B 268 ASN B 277 -1 N GLY B 273 O SER B 296 SHEET 7 AA4 9 ASN B 251 THR B 265 -1 N ALA B 259 O TYR B 274 SHEET 8 AA4 9 LEU B 280 ARG B 282 -1 O GLU B 281 N LYS B 253 SHEET 9 AA4 9 LYS B 285 LEU B 287 -1 O LEU B 287 N LEU B 280 SHEET 1 AA515 GLY C 47 ASN C 52 0 SHEET 2 AA515 GLU C 20 ASP C 35 -1 N GLN C 28 O ASN C 51 SHEET 3 AA515 ARG C 55 LYS C 62 -1 O GLY C 57 N TYR C 22 SHEET 4 AA515 THR C 70 GLU C 76 -1 O ILE C 75 N PHE C 58 SHEET 5 AA515 THR C 96 SER C 102 -1 O GLY C 99 N ILE C 72 SHEET 6 AA515 GLY C 106 LEU C 114 -1 O LEU C 110 N VAL C 98 SHEET 7 AA515 ARG C 148 ASP C 156 -1 O ASP C 156 N GLN C 107 SHEET 8 AA515 PHE C 164 ALA C 172 -1 O ALA C 168 N TRP C 155 SHEET 9 AA515 TYR C 184 LEU C 194 -1 O GLY C 187 N ALA C 169 SHEET 10 AA515 LEU C 197 ALA C 211 -1 O ALA C 201 N ALA C 190 SHEET 11 AA515 GLN C 214 TRP C 228 -1 O ASN C 218 N ASN C 206 SHEET 12 AA515 ILE C 233 ALA C 246 -1 O GLU C 243 N ASN C 219 SHEET 13 AA515 ASN C 251 THR C 265 -1 O GLU C 252 N ALA C 244 SHEET 14 AA515 GLU C 281 ARG C 282 -1 O GLU C 281 N LYS C 253 SHEET 15 AA515 LYS C 285 THR C 286 -1 O LYS C 285 N ARG C 282 SHEET 1 AA6 9 GLY C 47 ASN C 52 0 SHEET 2 AA6 9 GLU C 20 ASP C 35 -1 N GLN C 28 O ASN C 51 SHEET 3 AA6 9 ASP C 338 TYR C 349 -1 O ASP C 338 N ASP C 35 SHEET 4 AA6 9 ALA C 307 ASP C 317 -1 N ARG C 314 O GLU C 341 SHEET 5 AA6 9 ASP C 292 ASP C 304 -1 N ASP C 293 O ASP C 317 SHEET 6 AA6 9 TRP C 268 ASN C 277 -1 N ASN C 277 O ASP C 292 SHEET 7 AA6 9 ASN C 251 THR C 265 -1 N ALA C 259 O TYR C 274 SHEET 8 AA6 9 GLU C 281 ARG C 282 -1 O GLU C 281 N LYS C 253 SHEET 9 AA6 9 LYS C 285 THR C 286 -1 O LYS C 285 N ARG C 282 LINK O ASP A 43 NA NA A 403 1555 1555 2.64 LINK O ASN A 44 NA NA A 403 1555 1555 2.36 LINK O GLY A 46 NA NA A 403 1555 1555 2.50 LINK OE1 GLN A 107 NA NA A 404 1555 1555 3.12 LINK OE1 GLN A 146 NA NA A 402 1555 1555 2.41 LINK OE1 GLN A 149 NA NA A 402 1555 1555 2.63 LINK O ARG A 154 NA NA A 404 1555 1555 2.96 LINK OD2 ASP A 156 NA NA A 404 1555 1555 2.72 LINK OD1 ASP A 174 NA NA A 402 1555 1555 2.82 LINK NA NA A 403 O GLY C 181 1555 1555 2.75 LINK O ASN B 44 NA NA B 403 1555 1555 3.02 LINK O GLY B 46 NA NA B 403 1555 1555 2.79 LINK O PRO B 82 NA NA B 402 1555 1555 2.90 LINK O GLY B 85 NA NA B 402 1555 1555 2.98 LINK OD1 ASP B 174 NA NA B 404 1555 1555 2.93 LINK O GLY B 181 NA NA C 403 1555 1555 2.83 LINK O ASP C 43 NA NA C 403 1555 1555 2.82 LINK O ASN C 44 NA NA C 403 1555 1555 2.69 LINK O GLY C 46 NA NA C 403 1555 1555 2.30 LINK OE1 GLN C 146 NA NA C 402 1555 1555 2.79 LINK OE1 GLN C 149 NA NA C 402 1555 1555 2.63 LINK OD1 ASP C 174 NA NA C 402 1555 1555 2.98 LINK OD2 ASP C 174 NA NA C 402 1555 1555 3.12 CISPEP 1 TRP A 123 PRO A 124 0 11.62 CISPEP 2 ASN A 127 PRO A 128 0 2.39 CISPEP 3 TRP B 123 PRO B 124 0 16.85 CISPEP 4 ASN B 127 PRO B 128 0 3.56 CISPEP 5 TRP C 123 PRO C 124 0 14.52 CISPEP 6 ASN C 127 PRO C 128 0 2.52 CRYST1 86.326 134.103 145.787 90.00 90.00 90.00 P 21 21 21 12 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 0.011584 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007457 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006859 0.00000