HEADER HYDROLASE 23-OCT-18 6HZJ TITLE APO STRUCTURE OF TP DOMAIN FROM CLINICAL PENICILLIN-RESISTANT MUTANT TITLE 2 NEISSERIA GONORRHOEA STRAIN 6140 PENICILLIN-BINDING PROTEIN 2 (PBP2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE PEPTIDOGLYCAN D,D-TRANSPEPTIDASE PENA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PENICILLIN-BINDING PROTEIN 2,PBP-2; COMPND 5 EC: 3.4.16.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE FA6140; SOURCE 3 ORGANISM_TAXID: 528353; SOURCE 4 GENE: PENA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PENICILLIN-BINDING PROTEIN, TRANSPEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.BELLINI,L.KOEKEMOER,H.NEWMAN,C.G.DOWSON REVDAT 3 24-JAN-24 6HZJ 1 REMARK REVDAT 2 19-FEB-20 6HZJ 1 JRNL REVDAT 1 20-NOV-19 6HZJ 0 JRNL AUTH D.BELLINI,L.KOEKEMOER,H.NEWMAN,C.G.DOWSON JRNL TITL NOVEL AND IMPROVED CRYSTAL STRUCTURES OF H. INFLUENZAE, E. JRNL TITL 2 COLI AND P. AERUGINOSA PENICILLIN-BINDING PROTEIN 3 (PBP3) JRNL TITL 3 AND N. GONORRHOEAE PBP2: TOWARD A BETTER UNDERSTANDING OF JRNL TITL 4 BETA-LACTAM TARGET-MEDIATED RESISTANCE. JRNL REF J.MOL.BIOL. V. 431 3501 2019 JRNL REFN ESSN 1089-8638 JRNL PMID 31301409 JRNL DOI 10.1016/J.JMB.2019.07.010 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 104114 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) : 0.279 REMARK 3 R VALUE (WORKING SET) : 0.278 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5428 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) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5196 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.5150 REMARK 3 BIN FREE R VALUE SET COUNT : 262 REMARK 3 BIN FREE R VALUE : 0.5260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4968 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 405 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.36000 REMARK 3 B22 (A**2) : -0.92000 REMARK 3 B33 (A**2) : -1.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.474 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5067 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6867 ; 1.264 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 5.942 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 210 ;32.752 ;23.048 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 843 ;12.720 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;18.407 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 772 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3836 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 115424 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 56.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 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: MRBUMP REMARK 200 STARTING MODEL: 4U3T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M SODIUM CITRATE AND 0.1 M SODIUM REMARK 280 CACODYLATE PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 294K 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 38.79700 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 230 REMARK 465 PRO A 231 REMARK 465 GLY A 232 REMARK 465 TYR A 233 REMARK 465 GLN A 234 REMARK 465 ASP A 235 REMARK 465 GLY A 297 REMARK 465 ALA A 576 REMARK 465 VAL A 577 REMARK 465 LYS A 578 REMARK 465 THR A 579 REMARK 465 PRO A 580 REMARK 465 SER A 581 REMARK 465 GLY B 230 REMARK 465 PRO B 231 REMARK 465 GLY B 232 REMARK 465 TYR B 233 REMARK 465 GLN B 234 REMARK 465 GLY B 297 REMARK 465 ALA B 576 REMARK 465 VAL B 577 REMARK 465 LYS B 578 REMARK 465 THR B 579 REMARK 465 PRO B 580 REMARK 465 SER B 581 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PRO A 412 O HOH A 601 1.80 REMARK 500 O HOH B 777 O HOH B 806 1.91 REMARK 500 O HOH B 704 O HOH B 806 2.08 REMARK 500 N GLY B 458 O HOH B 601 2.16 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 C ALA A 575 CB ASN B 333 2645 1.97 REMARK 500 CA ALA A 575 N ASN B 333 2645 1.98 REMARK 500 CA LEU A 332 CB ALA B 575 2646 2.02 REMARK 500 O HOH A 607 O HOH B 715 2645 2.18 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 ALA B 575 C - N - CA ANGL. DEV. = 15.9 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 HIS A 440 48.68 -91.64 REMARK 500 LEU A 447 148.50 78.50 REMARK 500 GLN A 452 112.68 -162.39 REMARK 500 TYR A 543 -11.01 -148.96 REMARK 500 HIS B 440 46.73 -95.21 REMARK 500 LEU B 447 157.93 80.27 REMARK 500 TYR B 543 -11.90 -141.83 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 ALA B 574 ALA B 575 31.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HZH RELATED DB: PDB REMARK 900 RELATED ID: 6HZI RELATED DB: PDB REMARK 900 RELATED ID: 4U3T RELATED DB: PDB DBREF 6HZJ A 238 581 UNP E5KLA8 E5KLA8_NEIGO 238 582 DBREF 6HZJ B 238 581 UNP E5KLA8 E5KLA8_NEIGO 238 582 SEQADV 6HZJ GLY A 230 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ PRO A 231 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ GLY A 232 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ TYR A 233 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ GLN A 234 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ ASP A 235 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ PRO A 236 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ ARG A 237 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ GLY A 297 UNP E5KLA8 ALA 283 CONFLICT SEQADV 6HZJ A UNP E5KLA8 TYR 284 DELETION SEQADV 6HZJ A UNP E5KLA8 ASP 285 DELETION SEQADV 6HZJ A UNP E5KLA8 PRO 286 DELETION SEQADV 6HZJ A UNP E5KLA8 ASN 287 DELETION SEQADV 6HZJ A UNP E5KLA8 ARG 288 DELETION SEQADV 6HZJ A UNP E5KLA8 PRO 289 DELETION SEQADV 6HZJ A UNP E5KLA8 GLY 290 DELETION SEQADV 6HZJ A UNP E5KLA8 ARG 291 DELETION SEQADV 6HZJ A UNP E5KLA8 ALA 292 DELETION SEQADV 6HZJ A UNP E5KLA8 ASP 293 DELETION SEQADV 6HZJ A UNP E5KLA8 SER 294 DELETION SEQADV 6HZJ A UNP E5KLA8 GLU 295 DELETION SEQADV 6HZJ A UNP E5KLA8 GLN 296 DELETION SEQADV 6HZJ A UNP E5KLA8 ARG 297 DELETION SEQADV 6HZJ GLY B 230 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ PRO B 231 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ GLY B 232 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ TYR B 233 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ GLN B 234 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ ASP B 235 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ PRO B 236 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ ARG B 237 UNP E5KLA8 EXPRESSION TAG SEQADV 6HZJ GLY B 297 UNP E5KLA8 ALA 283 CONFLICT SEQADV 6HZJ B UNP E5KLA8 TYR 284 DELETION SEQADV 6HZJ B UNP E5KLA8 ASP 285 DELETION SEQADV 6HZJ B UNP E5KLA8 PRO 286 DELETION SEQADV 6HZJ B UNP E5KLA8 ASN 287 DELETION SEQADV 6HZJ B UNP E5KLA8 ARG 288 DELETION SEQADV 6HZJ B UNP E5KLA8 PRO 289 DELETION SEQADV 6HZJ B UNP E5KLA8 GLY 290 DELETION SEQADV 6HZJ B UNP E5KLA8 ARG 291 DELETION SEQADV 6HZJ B UNP E5KLA8 ALA 292 DELETION SEQADV 6HZJ B UNP E5KLA8 ASP 293 DELETION SEQADV 6HZJ B UNP E5KLA8 SER 294 DELETION SEQADV 6HZJ B UNP E5KLA8 GLU 295 DELETION SEQADV 6HZJ B UNP E5KLA8 GLN 296 DELETION SEQADV 6HZJ B UNP E5KLA8 ARG 297 DELETION SEQRES 1 A 339 GLY PRO GLY TYR GLN ASP PRO ARG SER LEU ASP GLN ARG SEQRES 2 A 339 ILE GLN THR LEU ALA TYR GLU GLU LEU ASN LYS ALA VAL SEQRES 3 A 339 GLU TYR HIS GLN ALA LYS ALA GLY THR VAL VAL VAL LEU SEQRES 4 A 339 ASP ALA ARG THR GLY GLU ILE LEU ALA LEU ALA ASN THR SEQRES 5 A 339 PRO GLY ARG ASN ARG ALA VAL THR ASP MET ILE GLU PRO SEQRES 6 A 339 GLY SER ALA ILE LYS PRO PHE VAL ILE ALA LYS ALA LEU SEQRES 7 A 339 ASP ALA GLY LYS THR ASP LEU ASN GLU ARG LEU ASN THR SEQRES 8 A 339 GLN PRO TYR LYS ILE GLY PRO SER PRO VAL ARG ASP ASP SEQRES 9 A 339 THR HIS VAL TYR PRO SER LEU ASP VAL ARG GLY ILE MET SEQRES 10 A 339 GLN LYS SER SER ASN VAL GLY THR SER LYS LEU SER ALA SEQRES 11 A 339 ARG PHE GLY ALA GLU GLU MET TYR ASP PHE TYR HIS GLU SEQRES 12 A 339 LEU GLY ILE GLY VAL ARG MET HIS SER GLY PHE PRO GLY SEQRES 13 A 339 GLU THR ALA GLY LEU LEU ARG ASN TRP ARG ARG TRP ARG SEQRES 14 A 339 PRO ILE GLU GLN ALA THR MET SER PHE GLY TYR GLY LEU SEQRES 15 A 339 GLN LEU SER LEU LEU GLN LEU ALA ARG ALA TYR THR ALA SEQRES 16 A 339 LEU THR HIS ASP GLY VAL LEU LEU PRO LEU SER PHE GLU SEQRES 17 A 339 LYS GLN ALA VAL ALA PRO GLN GLY LYS ARG ILE PHE LYS SEQRES 18 A 339 GLU SER THR ALA ARG GLU VAL ARG ASN LEU MET VAL SER SEQRES 19 A 339 VAL THR GLU PRO GLY GLY THR GLY THR ALA GLY ALA VAL SEQRES 20 A 339 ASP GLY PHE ASP VAL GLY ALA LYS THR GLY THR ALA ARG SEQRES 21 A 339 LYS LEU VAL ASN GLY ARG TYR VAL ASP ASN LYS HIS VAL SEQRES 22 A 339 GLY THR PHE ILE GLY PHE ALA PRO ALA LYS ASN PRO ARG SEQRES 23 A 339 VAL ILE VAL ALA VAL THR ILE ASP GLU PRO THR ALA HIS SEQRES 24 A 339 GLY TYR TYR GLY GLY VAL VAL ALA GLY SER PRO PHE LYS SEQRES 25 A 339 LYS ILE MET GLY GLY SER LEU ASN ILE LEU GLY ILE SER SEQRES 26 A 339 PRO THR LYS PRO LEU THR ALA ALA ALA VAL LYS THR PRO SEQRES 27 A 339 SER SEQRES 1 B 339 GLY PRO GLY TYR GLN ASP PRO ARG SER LEU ASP GLN ARG SEQRES 2 B 339 ILE GLN THR LEU ALA TYR GLU GLU LEU ASN LYS ALA VAL SEQRES 3 B 339 GLU TYR HIS GLN ALA LYS ALA GLY THR VAL VAL VAL LEU SEQRES 4 B 339 ASP ALA ARG THR GLY GLU ILE LEU ALA LEU ALA ASN THR SEQRES 5 B 339 PRO GLY ARG ASN ARG ALA VAL THR ASP MET ILE GLU PRO SEQRES 6 B 339 GLY SER ALA ILE LYS PRO PHE VAL ILE ALA LYS ALA LEU SEQRES 7 B 339 ASP ALA GLY LYS THR ASP LEU ASN GLU ARG LEU ASN THR SEQRES 8 B 339 GLN PRO TYR LYS ILE GLY PRO SER PRO VAL ARG ASP ASP SEQRES 9 B 339 THR HIS VAL TYR PRO SER LEU ASP VAL ARG GLY ILE MET SEQRES 10 B 339 GLN LYS SER SER ASN VAL GLY THR SER LYS LEU SER ALA SEQRES 11 B 339 ARG PHE GLY ALA GLU GLU MET TYR ASP PHE TYR HIS GLU SEQRES 12 B 339 LEU GLY ILE GLY VAL ARG MET HIS SER GLY PHE PRO GLY SEQRES 13 B 339 GLU THR ALA GLY LEU LEU ARG ASN TRP ARG ARG TRP ARG SEQRES 14 B 339 PRO ILE GLU GLN ALA THR MET SER PHE GLY TYR GLY LEU SEQRES 15 B 339 GLN LEU SER LEU LEU GLN LEU ALA ARG ALA TYR THR ALA SEQRES 16 B 339 LEU THR HIS ASP GLY VAL LEU LEU PRO LEU SER PHE GLU SEQRES 17 B 339 LYS GLN ALA VAL ALA PRO GLN GLY LYS ARG ILE PHE LYS SEQRES 18 B 339 GLU SER THR ALA ARG GLU VAL ARG ASN LEU MET VAL SER SEQRES 19 B 339 VAL THR GLU PRO GLY GLY THR GLY THR ALA GLY ALA VAL SEQRES 20 B 339 ASP GLY PHE ASP VAL GLY ALA LYS THR GLY THR ALA ARG SEQRES 21 B 339 LYS LEU VAL ASN GLY ARG TYR VAL ASP ASN LYS HIS VAL SEQRES 22 B 339 GLY THR PHE ILE GLY PHE ALA PRO ALA LYS ASN PRO ARG SEQRES 23 B 339 VAL ILE VAL ALA VAL THR ILE ASP GLU PRO THR ALA HIS SEQRES 24 B 339 GLY TYR TYR GLY GLY VAL VAL ALA GLY SER PRO PHE LYS SEQRES 25 B 339 LYS ILE MET GLY GLY SER LEU ASN ILE LEU GLY ILE SER SEQRES 26 B 339 PRO THR LYS PRO LEU THR ALA ALA ALA VAL LYS THR PRO SEQRES 27 B 339 SER FORMUL 3 HOH *405(H2 O) HELIX 1 AA1 ASP A 240 HIS A 258 1 19 HELIX 2 AA2 ASN A 299 ASP A 304 1 6 HELIX 3 AA3 PRO A 308 ALA A 311 5 4 HELIX 4 AA4 ILE A 312 ALA A 323 1 12 HELIX 5 AA5 VAL A 355 LYS A 361 1 7 HELIX 6 AA6 SER A 363 ALA A 372 1 10 HELIX 7 AA7 GLY A 375 LEU A 386 1 12 HELIX 8 AA8 ASN A 406 TRP A 410 5 5 HELIX 9 AA9 ARG A 411 PHE A 420 1 10 HELIX 10 AB1 LEU A 428 HIS A 440 1 13 HELIX 11 AB2 LYS A 463 VAL A 475 1 13 HELIX 12 AB3 SER A 476 THR A 478 5 3 HELIX 13 AB4 GLY A 484 ALA A 488 5 5 HELIX 14 AB5 TYR A 544 LEU A 564 1 21 HELIX 15 AB6 ASP B 240 HIS B 258 1 19 HELIX 16 AB7 ASN B 299 ASP B 304 1 6 HELIX 17 AB8 PRO B 308 ALA B 311 5 4 HELIX 18 AB9 ILE B 312 ALA B 323 1 12 HELIX 19 AC1 VAL B 355 SER B 362 1 8 HELIX 20 AC2 SER B 363 ALA B 372 1 10 HELIX 21 AC3 GLY B 375 LEU B 386 1 12 HELIX 22 AC4 ASN B 406 TRP B 410 5 5 HELIX 23 AC5 ARG B 411 PHE B 420 1 10 HELIX 24 AC6 LEU B 428 HIS B 440 1 13 HELIX 25 AC7 LYS B 463 VAL B 475 1 13 HELIX 26 AC8 SER B 476 THR B 478 5 3 HELIX 27 AC9 GLY B 484 ALA B 488 5 5 HELIX 28 AD1 TYR B 544 LEU B 564 1 21 SHEET 1 AA1 5 ILE A 275 ASN A 280 0 SHEET 2 AA1 5 ALA A 262 ASP A 269 -1 N VAL A 265 O ALA A 279 SHEET 3 AA1 5 VAL A 529 ASP A 536 -1 O ALA A 532 N VAL A 266 SHEET 4 AA1 5 TYR A 509 ALA A 522 -1 N GLY A 516 O ILE A 535 SHEET 5 AA1 5 GLY A 495 LEU A 504 -1 N GLY A 499 O THR A 517 SHEET 1 AA2 2 MET A 305 ILE A 306 0 SHEET 2 AA2 2 LEU A 426 SER A 427 -1 O LEU A 426 N ILE A 306 SHEET 1 AA3 2 ARG A 331 ASN A 333 0 SHEET 2 AA3 2 SER A 352 ASP A 354 -1 O LEU A 353 N LEU A 332 SHEET 1 AA4 2 TYR A 337 ILE A 339 0 SHEET 2 AA4 2 SER A 342 VAL A 344 -1 O SER A 342 N ILE A 339 SHEET 1 AA5 2 VAL A 443 LEU A 444 0 SHEET 2 AA5 2 LYS A 459 ARG A 460 -1 O LYS A 459 N LEU A 444 SHEET 1 AA6 5 ILE B 275 ASN B 280 0 SHEET 2 AA6 5 ALA B 262 ASP B 269 -1 N VAL B 265 O ALA B 279 SHEET 3 AA6 5 VAL B 529 ASP B 536 -1 O ALA B 532 N VAL B 266 SHEET 4 AA6 5 ARG B 508 ALA B 522 -1 N GLY B 516 O ILE B 535 SHEET 5 AA6 5 GLY B 495 VAL B 505 -1 N GLY B 495 O PHE B 521 SHEET 1 AA7 2 MET B 305 ILE B 306 0 SHEET 2 AA7 2 LEU B 426 SER B 427 -1 O LEU B 426 N ILE B 306 SHEET 1 AA8 2 ARG B 331 ASN B 333 0 SHEET 2 AA8 2 SER B 352 ASP B 354 -1 O LEU B 353 N LEU B 332 SHEET 1 AA9 2 TYR B 337 ILE B 339 0 SHEET 2 AA9 2 SER B 342 VAL B 344 -1 O VAL B 344 N TYR B 337 SHEET 1 AB1 2 VAL B 443 LEU B 444 0 SHEET 2 AB1 2 LYS B 459 ARG B 460 -1 O LYS B 459 N LEU B 444 CISPEP 1 ALA A 522 PRO A 523 0 -9.40 CISPEP 2 ALA B 522 PRO B 523 0 -8.50 CRYST1 52.645 77.594 81.866 90.00 98.61 90.00 P 1 21 1 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 0.018995 0.000000 0.002876 0.00000 SCALE2 0.000000 0.012888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012354 0.00000