HEADER BIOSYNTHETIC PROTEIN 11-JAN-11 2Y4Y TITLE STRUCTURE OF A DOMAIN FROM THE TYPE IV PILUS BIOGENESIS LIPOPROTEIN TITLE 2 PILP, FROM PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PILP PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESIDUES 83-171; COMPND 5 SYNONYM: PILP, TYPE 4 FIMBRIAL BIOGENESIS PROTEIN PILP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.P.DERRICK,J.BERRY REVDAT 1 18-JAN-12 2Y4Y 0 JRNL AUTH J.BERRY,J.P.DERRICK JRNL TITL STRUCTURE OF A DOMAIN FROM THE TYPE IV PILUS BIOGENESIS JRNL TITL 2 LIPOPROTEIN PILP, FROM PSEUDOMONAS AERUGINOSA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 44944 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 FREE R VALUE TEST SET COUNT : 2422 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3235 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 179 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 299 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : -0.01 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : -0.05 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.782 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2527 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3384 ; 2.298 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 314 ; 6.580 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;36.730 ;23.091 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 466 ;13.261 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.402 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 384 ; 0.199 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1864 ; 0.011 ; 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): 1572 ; 2.571 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2506 ; 3.693 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 955 ; 5.710 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 874 ; 7.792 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2527 ; 3.288 ; 3.000 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 : 1.40 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 2Y4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-11. REMARK 100 THE PDBE ID CODE IS EBI-46857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2822 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 4) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47367 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.70 REMARK 200 RESOLUTION RANGE LOW (A) : 32.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 7.3 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.90 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CRANK REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 8.5, 0.6M ZINC ACETATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 51.60000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.60000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.25500 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -410.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 59.80784 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 60.16471 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 A2027 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 GLY A 79 REMARK 465 SER A 80 REMARK 465 HIS A 81 REMARK 465 MET A 82 REMARK 465 GLU A 145 REMARK 465 GLY A 146 REMARK 465 ASP A 156 REMARK 465 GLY A 157 REMARK 465 GLU A 158 REMARK 465 GLY A 159 REMARK 465 ASN A 160 REMARK 465 GLY B 79 REMARK 465 SER B 80 REMARK 465 HIS B 81 REMARK 465 MET B 82 REMARK 465 ILE B 83 REMARK 465 LYS B 84 REMARK 465 PRO B 85 REMARK 465 ASP B 86 REMARK 465 GLU B 87 REMARK 465 THR B 88 REMARK 465 PRO B 155 REMARK 465 ASP B 156 REMARK 465 GLY B 157 REMARK 465 GLU B 158 REMARK 465 GLY B 159 REMARK 465 ASN B 160 REMARK 465 TRP B 161 REMARK 465 GLY C 79 REMARK 465 SER C 80 REMARK 465 ILE C 83 REMARK 465 LYS C 84 REMARK 465 PRO C 85 REMARK 465 ASP C 86 REMARK 465 GLU C 87 REMARK 465 THR C 88 REMARK 465 PRO C 155 REMARK 465 ASP C 156 REMARK 465 GLY C 157 REMARK 465 GLU C 158 REMARK 465 GLY C 159 REMARK 465 ASN C 160 REMARK 465 GLY D 79 REMARK 465 SER D 80 REMARK 465 HIS D 81 REMARK 465 MET D 82 REMARK 465 ILE D 83 REMARK 465 GLU D 87 REMARK 465 THR D 88 REMARK 465 ASP D 156 REMARK 465 GLY D 157 REMARK 465 GLU D 158 REMARK 465 GLY D 159 REMARK 465 ASN D 160 REMARK 465 LYS D 171 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 HOH D 2062 O HOH D 2063 1.82 REMARK 500 O HOH A 2001 O HOH A 2087 1.95 REMARK 500 O HOH C 2039 O HOH C 2077 1.99 REMARK 500 O HOH D 2061 O HOH D 2064 2.05 REMARK 500 O HOH A 2026 O HOH A 2039 2.11 REMARK 500 N TRP A 161 O HOH A 2069 2.15 REMARK 500 O HOH B 2005 O HOH B 2048 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 126 CG ARG B 126 CD -0.166 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 ARG A 166 CB - CA - C ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG B 89 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 128 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 HIS C 81 CB - CA - C ANGL. DEV. = 19.2 DEGREES REMARK 500 MET C 82 CB - CG - SD ANGL. DEV. = 22.5 DEGREES REMARK 500 ARG D 128 NE - CZ - NH2 ANGL. DEV. = 3.4 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 SER B 144 142.06 -171.01 REMARK 500 SER C 144 138.83 -174.22 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 HIS C 81 MET C 82 -147.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 MET C 82 20.7 L L OUTSIDE RANGE 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 ZN A1172 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 125 ND1 REMARK 620 2 GLU C 103 OE1 103.8 REMARK 620 3 ACT A1176 O 119.2 87.3 REMARK 620 4 HOH A2084 O 110.2 124.4 111.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1172 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2068 O REMARK 620 2 HIS B 125 ND1 117.0 REMARK 620 3 HIS B 125 ND1 86.7 121.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1172 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 103 OE1 REMARK 620 2 HIS C 125 ND1 96.0 REMARK 620 3 HOH C2076 O 131.4 109.6 REMARK 620 4 HOH C2077 O 102.0 118.0 101.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1172 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D2061 O REMARK 620 2 GLU A 103 OE1 126.7 REMARK 620 3 HIS D 125 ND1 107.7 94.0 REMARK 620 4 HOH D2062 O 102.2 103.7 124.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1175 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2086 O REMARK 620 2 GLU D 163 OE2 104.0 REMARK 620 3 GLU A 163 OE2 107.4 121.7 REMARK 620 4 HOH A2087 O 106.7 112.9 103.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1173 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 163 OE1 REMARK 620 2 GLU C 163 OE1 97.4 REMARK 620 3 HOH B2069 O 100.7 109.5 REMARK 620 4 HIS C 81 ND1 116.3 116.0 114.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1174 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1175 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1176 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C1172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C1173 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C1174 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT D1171 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D1172 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y4X RELATED DB: PDB REMARK 900 STRUCTURE OF A DOMAIN FROM THE TYPE IV PILUS BIOGENESIS REMARK 900 LIPOPROTEIN PILP, FROM PSEUDOMONAS AERUGINOSA PA01 REMARK 999 REMARK 999 SEQUENCE REMARK 999 GSHM IS FROM THE EXPRESSION VECTOR (PET15B) AFTER THROMBIN REMARK 999 CLEAVAGE DBREF 2Y4Y A 83 171 UNP Q51354 Q51354_PSEAE 83 171 DBREF 2Y4Y B 83 171 UNP Q51354 Q51354_PSEAE 83 171 DBREF 2Y4Y C 83 171 UNP Q51354 Q51354_PSEAE 83 171 DBREF 2Y4Y D 83 171 UNP Q51354 Q51354_PSEAE 83 171 SEQADV 2Y4Y GLY A 79 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y SER A 80 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y HIS A 81 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y MET A 82 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y GLY B 79 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y SER B 80 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y HIS B 81 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y MET B 82 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y GLY C 79 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y SER C 80 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y HIS C 81 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y MET C 82 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y GLY D 79 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y SER D 80 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y HIS D 81 UNP Q51354 EXPRESSION TAG SEQADV 2Y4Y MET D 82 UNP Q51354 EXPRESSION TAG SEQRES 1 A 93 GLY SER HIS MET ILE LYS PRO ASP GLU THR ARG VAL LYS SEQRES 2 A 93 GLN PHE LEU GLU GLY PHE ASN ILE GLU THR PHE GLU MET SEQRES 3 A 93 VAL GLY THR LEU SER ASN ALA GLN GLY THR PHE ALA LEU SEQRES 4 A 93 VAL LYS GLY ALA GLY GLY VAL HIS ARG VAL ARG VAL GLY SEQRES 5 A 93 ASP TYR LEU GLY ARG ASN ASP GLY LYS VAL VAL GLY ILE SEQRES 6 A 93 SER GLU GLY LYS ILE ASP VAL ILE GLU ILE VAL PRO ASP SEQRES 7 A 93 GLY GLU GLY ASN TRP LEU GLU ARG PRO ARG SER LEU THR SEQRES 8 A 93 LEU LYS SEQRES 1 B 93 GLY SER HIS MET ILE LYS PRO ASP GLU THR ARG VAL LYS SEQRES 2 B 93 GLN PHE LEU GLU GLY PHE ASN ILE GLU THR PHE GLU MET SEQRES 3 B 93 VAL GLY THR LEU SER ASN ALA GLN GLY THR PHE ALA LEU SEQRES 4 B 93 VAL LYS GLY ALA GLY GLY VAL HIS ARG VAL ARG VAL GLY SEQRES 5 B 93 ASP TYR LEU GLY ARG ASN ASP GLY LYS VAL VAL GLY ILE SEQRES 6 B 93 SER GLU GLY LYS ILE ASP VAL ILE GLU ILE VAL PRO ASP SEQRES 7 B 93 GLY GLU GLY ASN TRP LEU GLU ARG PRO ARG SER LEU THR SEQRES 8 B 93 LEU LYS SEQRES 1 C 93 GLY SER HIS MET ILE LYS PRO ASP GLU THR ARG VAL LYS SEQRES 2 C 93 GLN PHE LEU GLU GLY PHE ASN ILE GLU THR PHE GLU MET SEQRES 3 C 93 VAL GLY THR LEU SER ASN ALA GLN GLY THR PHE ALA LEU SEQRES 4 C 93 VAL LYS GLY ALA GLY GLY VAL HIS ARG VAL ARG VAL GLY SEQRES 5 C 93 ASP TYR LEU GLY ARG ASN ASP GLY LYS VAL VAL GLY ILE SEQRES 6 C 93 SER GLU GLY LYS ILE ASP VAL ILE GLU ILE VAL PRO ASP SEQRES 7 C 93 GLY GLU GLY ASN TRP LEU GLU ARG PRO ARG SER LEU THR SEQRES 8 C 93 LEU LYS SEQRES 1 D 93 GLY SER HIS MET ILE LYS PRO ASP GLU THR ARG VAL LYS SEQRES 2 D 93 GLN PHE LEU GLU GLY PHE ASN ILE GLU THR PHE GLU MET SEQRES 3 D 93 VAL GLY THR LEU SER ASN ALA GLN GLY THR PHE ALA LEU SEQRES 4 D 93 VAL LYS GLY ALA GLY GLY VAL HIS ARG VAL ARG VAL GLY SEQRES 5 D 93 ASP TYR LEU GLY ARG ASN ASP GLY LYS VAL VAL GLY ILE SEQRES 6 D 93 SER GLU GLY LYS ILE ASP VAL ILE GLU ILE VAL PRO ASP SEQRES 7 D 93 GLY GLU GLY ASN TRP LEU GLU ARG PRO ARG SER LEU THR SEQRES 8 D 93 LEU LYS HET ZN A1172 1 HET ACT A1173 4 HET ACT A1174 4 HET ZN A1175 1 HET ACT A1176 4 HET ZN C1172 1 HET ZN B1172 1 HET ZN B1173 1 HET ACT C1173 4 HET ACT C1174 4 HET ACT D1171 4 HET ZN D1172 1 HETNAM ZN ZINC ION HETNAM ACT ACETATE ION FORMUL 5 ZN 6(ZN 2+) FORMUL 6 ACT 6(C2 H3 O2 1-) FORMUL 7 HOH *299(H2 O) HELIX 1 1 GLN A 92 PHE A 97 5 6 HELIX 2 2 ASN A 98 PHE A 102 5 5 HELIX 3 3 GLN B 92 PHE B 97 5 6 HELIX 4 4 ASN B 98 PHE B 102 5 5 HELIX 5 5 GLN C 92 PHE C 97 5 6 HELIX 6 6 ASN C 98 PHE C 102 5 5 HELIX 7 7 GLN D 92 PHE D 97 5 6 HELIX 8 8 ASN D 98 PHE D 102 5 5 SHEET 1 AA 3 GLU A 103 ASN A 110 0 SHEET 2 AA 3 GLY A 113 GLY A 120 -1 O GLY A 113 N ASN A 110 SHEET 3 AA 3 GLY A 123 VAL A 127 -1 O GLY A 123 N GLY A 120 SHEET 1 AB 4 TYR A 132 LEU A 133 0 SHEET 2 AB 4 GLY A 138 ILE A 143 -1 O GLY A 138 N LEU A 133 SHEET 3 AB 4 ILE A 148 VAL A 154 -1 O ASP A 149 N VAL A 141 SHEET 4 AB 4 LEU A 162 LEU A 168 -1 O LEU A 162 N VAL A 154 SHEET 1 BA 3 GLU B 103 ASN B 110 0 SHEET 2 BA 3 GLY B 113 GLY B 120 -1 O GLY B 113 N ASN B 110 SHEET 3 BA 3 GLY B 123 VAL B 127 -1 O GLY B 123 N GLY B 120 SHEET 1 BB 4 TYR B 132 LEU B 133 0 SHEET 2 BB 4 GLY B 138 SER B 144 -1 O GLY B 138 N LEU B 133 SHEET 3 BB 4 LYS B 147 ILE B 153 -1 O LYS B 147 N SER B 144 SHEET 4 BB 4 GLU B 163 THR B 169 -1 O ARG B 164 N GLU B 152 SHEET 1 CA 3 GLU C 103 ASN C 110 0 SHEET 2 CA 3 GLY C 113 GLY C 120 -1 O GLY C 113 N ASN C 110 SHEET 3 CA 3 GLY C 123 VAL C 127 -1 O GLY C 123 N GLY C 120 SHEET 1 CB 4 TYR C 132 LEU C 133 0 SHEET 2 CB 4 GLY C 138 SER C 144 -1 O GLY C 138 N LEU C 133 SHEET 3 CB 4 LYS C 147 ILE C 153 -1 O LYS C 147 N SER C 144 SHEET 4 CB 4 GLU C 163 THR C 169 -1 O ARG C 164 N GLU C 152 SHEET 1 DA 3 GLU D 103 ASN D 110 0 SHEET 2 DA 3 GLY D 113 GLY D 120 -1 O GLY D 113 N ASN D 110 SHEET 3 DA 3 GLY D 123 VAL D 127 -1 O GLY D 123 N GLY D 120 SHEET 1 DB 4 TYR D 132 LEU D 133 0 SHEET 2 DB 4 GLY D 138 SER D 144 -1 O GLY D 138 N LEU D 133 SHEET 3 DB 4 LYS D 147 VAL D 154 -1 O LYS D 147 N SER D 144 SHEET 4 DB 4 LEU D 162 THR D 169 -1 O LEU D 162 N VAL D 154 LINK ZN ZN A1172 ND1 HIS A 125 1555 1555 1.96 LINK ZN ZN A1172 OE1 GLU C 103 1555 1555 2.06 LINK ZN ZN A1172 O ACT A1176 1555 1555 2.00 LINK ZN ZN A1172 O HOH A2084 1555 1555 2.02 LINK ZN ZN A1175 O HOH A2086 1555 1555 2.49 LINK ZN ZN A1175 OE2 GLU D 163 1555 4555 1.98 LINK ZN ZN A1175 OE2 GLU A 163 1555 1555 2.06 LINK ZN ZN A1175 O HOH A2087 1555 1555 2.13 LINK ZN ZN B1172 ND1 HIS B 125 1555 1555 2.53 LINK ZN ZN B1172 ND1 HIS B 125 1555 2656 2.51 LINK ZN ZN B1172 O HOH B2068 1555 1555 2.53 LINK ZN ZN B1173 OE1 GLU C 163 1555 4646 1.85 LINK ZN ZN B1173 O HOH B2069 1555 1555 2.20 LINK ZN ZN B1173 ND1 HIS C 81 1555 4646 2.14 LINK ZN ZN B1173 OE1 GLU B 163 1555 1555 2.11 LINK OE1 GLU C 163 ZN ZN B1173 1555 4656 1.85 LINK ZN ZN C1172 O HOH C2077 1555 1555 2.15 LINK ZN ZN C1172 O HOH C2076 1555 1555 2.00 LINK ZN ZN C1172 ND1 HIS C 125 1555 1555 2.07 LINK ZN ZN C1172 OE1 GLU B 103 1555 1555 2.01 LINK ZN ZN D1172 O HOH D2062 1555 1555 2.03 LINK ZN ZN D1172 ND1 HIS D 125 1555 1555 2.04 LINK ZN ZN D1172 OE1 GLU A 103 1555 1555 2.02 LINK ZN ZN D1172 O HOH D2061 1555 1555 2.01 SITE 1 AC1 4 HIS A 125 ACT A1176 HOH A2084 GLU C 103 SITE 1 AC2 3 ASN A 110 ARG A 126 HOH A2085 SITE 1 AC3 2 ARG A 126 ACT C1174 SITE 1 AC4 4 GLU A 163 HOH A2086 HOH A2087 GLU D 163 SITE 1 AC5 6 HIS A 125 ARG A 126 ZN A1172 HOH A2089 SITE 2 AC5 6 GLU C 103 VAL C 105 SITE 1 AC6 4 GLU B 103 HIS C 125 HOH C2076 HOH C2077 SITE 1 AC7 2 HIS B 125 HOH B2068 SITE 1 AC8 4 GLU B 163 HOH B2069 HIS C 81 GLU C 163 SITE 1 AC9 3 VAL A 105 ASN C 110 ARG C 126 SITE 1 BC1 3 ACT A1174 ARG C 126 HOH C2037 SITE 1 BC2 3 VAL B 105 ASN D 110 ARG D 126 SITE 1 BC3 5 GLU A 103 HIS D 125 HOH D2061 HOH D2062 SITE 2 BC3 5 HOH D2063 CRYST1 103.200 74.510 74.180 90.00 125.80 90.00 C 1 2 1 16 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 0.009690 0.000000 0.006989 0.00000 SCALE2 0.000000 0.013421 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016621 0.00000 MTRIX1 1 -0.413100 -0.178900 -0.892900 77.36000 1 MTRIX2 1 0.205200 -0.973600 0.100100 25.52000 1 MTRIX3 1 -0.887300 -0.141900 0.438900 37.15000 1 MTRIX1 2 0.331300 -0.846800 -0.416200 50.47000 1 MTRIX2 2 0.855400 0.083430 0.511300 -24.66000 1 MTRIX3 2 -0.398200 -0.525400 0.751900 24.34000 1 MTRIX1 3 0.340600 0.833400 -0.435200 14.79000 1 MTRIX2 3 -0.835100 0.055540 -0.547200 57.98000 1 MTRIX3 3 -0.431900 0.549900 0.714900 15.24000 1