PDB Short entry for 2O6D HEADER MEMBRANE PROTEIN, PROTEIN BINDING 07-DEC-06 2O6D TITLE STRUCTURE OF NATIVE RTP34 FROM TREPONEMA PALLIDUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 34 KDA MEMBRANE ANTIGEN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PATHOGEN-SPECIFIC MEMBRANE ANTIGEN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TREPONEMA PALLIDUM; SOURCE 3 ORGANISM_TAXID: 160; SOURCE 4 GENE: TPD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEXHTA KEYWDS IG-FOLD, SYPHILIS, METAL-ION BINDING, DIMER, MEMBRANE PROTEIN, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.MACHIUS,C.A.BRAUTIGAM,R.K.DEKA,D.R.TOMCHICK,S.B.LUMPKINS, AUTHOR 2 M.V.NORGARD REVDAT 7 03-APR-24 2O6D 1 REMARK REVDAT 6 27-DEC-23 2O6D 1 REMARK REVDAT 5 20-OCT-21 2O6D 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2O6D 1 VERSN REVDAT 3 24-FEB-09 2O6D 1 VERSN REVDAT 2 01-MAY-07 2O6D 1 JRNL REVDAT 1 26-DEC-06 2O6D 0 JRNL AUTH R.K.DEKA,C.A.BRAUTIGAM,F.L.TOMSON,S.B.LUMPKINS,D.R.TOMCHICK, JRNL AUTH 2 M.MACHIUS,M.V.NORGARD JRNL TITL CRYSTAL STRUCTURE OF THE TP34 (TP0971) LIPOPROTEIN OF JRNL TITL 2 TREPONEMA PALLIDUM: IMPLICATIONS OF ITS METAL-BOUND STATE JRNL TITL 3 AND AFFINITY FOR HUMAN LACTOFERRIN. JRNL REF J.BIOL.CHEM. V. 282 5944 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17192261 JRNL DOI 10.1074/JBC.M610215200 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 28200 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1418 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1549 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2485 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.39000 REMARK 3 B22 (A**2) : -1.11000 REMARK 3 B33 (A**2) : -0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.247 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2707 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3694 ; 1.972 ; 1.933 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 338 ; 4.345 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 142 ;34.305 ;24.789 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 397 ;14.706 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;22.141 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 350 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2539 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1104 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1741 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 164 ; 0.150 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.200 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 42 ; 0.216 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.197 ; 0.200 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): 1674 ; 0.989 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2641 ; 1.640 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1187 ; 2.534 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1053 ; 4.135 ; 4.500 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 : 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 28 A 185 REMARK 3 ORIGIN FOR THE GROUP (A): 10.8157 40.9831 61.2153 REMARK 3 T TENSOR REMARK 3 T11: -0.1111 T22: -0.0236 REMARK 3 T33: -0.0496 T12: -0.0015 REMARK 3 T13: -0.0035 T23: -0.0372 REMARK 3 L TENSOR REMARK 3 L11: 0.7421 L22: 1.5103 REMARK 3 L33: 2.0956 L12: 0.4724 REMARK 3 L13: 1.2004 L23: 1.0944 REMARK 3 S TENSOR REMARK 3 S11: -0.0032 S12: -0.0320 S13: -0.0108 REMARK 3 S21: -0.1146 S22: 0.0473 S23: 0.0108 REMARK 3 S31: -0.0543 S32: -0.0240 S33: -0.0441 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 29 B 185 REMARK 3 ORIGIN FOR THE GROUP (A): 6.4526 14.5920 52.3046 REMARK 3 T TENSOR REMARK 3 T11: 0.0457 T22: -0.0867 REMARK 3 T33: -0.0520 T12: -0.0246 REMARK 3 T13: -0.0897 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.8762 L22: 2.1301 REMARK 3 L33: 2.3207 L12: 0.8306 REMARK 3 L13: 0.9737 L23: 1.4835 REMARK 3 S TENSOR REMARK 3 S11: 0.1905 S12: -0.0957 S13: -0.0995 REMARK 3 S21: 0.2684 S22: -0.0299 S23: -0.1323 REMARK 3 S31: 0.2693 S32: -0.0792 S33: -0.1606 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 REMARK 4 REMARK 4 2O6D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97921 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI-111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28256 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 27.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.50800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: SE-MET PROTEIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M AMMONIUM SULFATE, 0.1 M BICINE, REMARK 280 PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 17.03550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.30250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.94050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.30250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.03550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.94050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -152.0 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 GLY A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 GLU A 6 REMARK 465 HIS A 7 REMARK 465 GLN A 8 REMARK 465 HIS A 9 REMARK 465 GLY A 10 REMARK 465 GLU A 11 REMARK 465 GLU A 12 REMARK 465 MET A 13 REMARK 465 MET A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 VAL A 17 REMARK 465 PRO A 18 REMARK 465 ALA A 19 REMARK 465 PRO A 20 REMARK 465 ASP A 21 REMARK 465 ALA A 22 REMARK 465 GLU A 23 REMARK 465 GLY A 24 REMARK 465 ALA A 25 REMARK 465 ALA A 26 REMARK 465 GLY A 27 REMARK 465 GLY B -3 REMARK 465 ALA B -2 REMARK 465 MET B -1 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 GLY B 3 REMARK 465 GLY B 4 REMARK 465 GLY B 5 REMARK 465 GLU B 6 REMARK 465 HIS B 7 REMARK 465 GLN B 8 REMARK 465 HIS B 9 REMARK 465 GLY B 10 REMARK 465 GLU B 11 REMARK 465 GLU B 12 REMARK 465 MET B 13 REMARK 465 MET B 14 REMARK 465 ALA B 15 REMARK 465 ALA B 16 REMARK 465 VAL B 17 REMARK 465 PRO B 18 REMARK 465 ALA B 19 REMARK 465 PRO B 20 REMARK 465 ASP B 21 REMARK 465 ALA B 22 REMARK 465 GLU B 23 REMARK 465 GLY B 24 REMARK 465 ALA B 25 REMARK 465 ALA B 26 REMARK 465 GLY B 27 REMARK 465 PHE B 28 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 139 OE1 GLU A 174 2.12 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 ASN B 78 -167.77 -106.54 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 80 GLY B 81 56.10 REMARK 500 THR B 160 GLY B 161 -113.85 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 A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 70 NE2 REMARK 620 2 MET A 117 SD 99.4 REMARK 620 3 HIS A 124 NE2 105.8 106.6 REMARK 620 4 HIS B 155 NE2 112.6 83.3 138.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 155 NE2 REMARK 620 2 HIS B 70 NE2 103.7 REMARK 620 3 MET B 117 SD 85.4 102.5 REMARK 620 4 HIS B 124 NE2 104.0 142.0 105.3 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 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O6C RELATED DB: PDB REMARK 900 RELATED ID: 2O6E RELATED DB: PDB REMARK 900 RELATED ID: 2O6F RELATED DB: PDB DBREF 2O6D A -3 185 UNP P19478 TA34_TREPA 16 204 DBREF 2O6D B -3 185 UNP P19478 TA34_TREPA 16 204 SEQADV 2O6D GLY A -3 UNP P19478 VAL 16 ENGINEERED MUTATION SEQADV 2O6D ALA A -2 UNP P19478 PHE 17 ENGINEERED MUTATION SEQADV 2O6D MET A -1 UNP P19478 SER 18 ENGINEERED MUTATION SEQADV 2O6D GLY A 0 UNP P19478 ALA 19 ENGINEERED MUTATION SEQADV 2O6D SER A 1 UNP P19478 CYS 20 ENGINEERED MUTATION SEQADV 2O6D GLY B -3 UNP P19478 VAL 16 ENGINEERED MUTATION SEQADV 2O6D ALA B -2 UNP P19478 PHE 17 ENGINEERED MUTATION SEQADV 2O6D MET B -1 UNP P19478 SER 18 ENGINEERED MUTATION SEQADV 2O6D GLY B 0 UNP P19478 ALA 19 ENGINEERED MUTATION SEQADV 2O6D SER B 1 UNP P19478 CYS 20 ENGINEERED MUTATION SEQRES 1 A 189 GLY ALA MET GLY SER GLY GLY GLY GLY GLU HIS GLN HIS SEQRES 2 A 189 GLY GLU GLU MET MET ALA ALA VAL PRO ALA PRO ASP ALA SEQRES 3 A 189 GLU GLY ALA ALA GLY PHE ASP GLU PHE PRO ILE GLY GLU SEQRES 4 A 189 ASP ARG ASP VAL GLY PRO LEU HIS VAL GLY GLY VAL TYR SEQRES 5 A 189 PHE GLN PRO VAL GLU MET HIS PRO ALA PRO GLY ALA GLN SEQRES 6 A 189 PRO SER LYS GLU GLU ALA ASP CYS HIS ILE GLU ALA ASP SEQRES 7 A 189 ILE HIS ALA ASN GLU ALA GLY LYS ASP LEU GLY TYR GLY SEQRES 8 A 189 VAL GLY ASP PHE VAL PRO TYR LEU ARG VAL VAL ALA PHE SEQRES 9 A 189 LEU GLN LYS HIS GLY SER GLU LYS VAL GLN LYS VAL MET SEQRES 10 A 189 PHE ALA PRO MET ASN ALA GLY ASP GLY PRO HIS TYR GLY SEQRES 11 A 189 ALA ASN VAL LYS PHE GLU GLU GLY LEU GLY THR TYR LYS SEQRES 12 A 189 VAL ARG PHE GLU ILE ALA ALA PRO SER HIS ASP GLU TYR SEQRES 13 A 189 SER LEU HIS ILE ASP GLU GLN THR GLY VAL SER GLY ARG SEQRES 14 A 189 PHE TRP SER GLU PRO LEU VAL ALA GLU TRP ASP ASP PHE SEQRES 15 A 189 GLU TRP LYS GLY PRO GLN TRP SEQRES 1 B 189 GLY ALA MET GLY SER GLY GLY GLY GLY GLU HIS GLN HIS SEQRES 2 B 189 GLY GLU GLU MET MET ALA ALA VAL PRO ALA PRO ASP ALA SEQRES 3 B 189 GLU GLY ALA ALA GLY PHE ASP GLU PHE PRO ILE GLY GLU SEQRES 4 B 189 ASP ARG ASP VAL GLY PRO LEU HIS VAL GLY GLY VAL TYR SEQRES 5 B 189 PHE GLN PRO VAL GLU MET HIS PRO ALA PRO GLY ALA GLN SEQRES 6 B 189 PRO SER LYS GLU GLU ALA ASP CYS HIS ILE GLU ALA ASP SEQRES 7 B 189 ILE HIS ALA ASN GLU ALA GLY LYS ASP LEU GLY TYR GLY SEQRES 8 B 189 VAL GLY ASP PHE VAL PRO TYR LEU ARG VAL VAL ALA PHE SEQRES 9 B 189 LEU GLN LYS HIS GLY SER GLU LYS VAL GLN LYS VAL MET SEQRES 10 B 189 PHE ALA PRO MET ASN ALA GLY ASP GLY PRO HIS TYR GLY SEQRES 11 B 189 ALA ASN VAL LYS PHE GLU GLU GLY LEU GLY THR TYR LYS SEQRES 12 B 189 VAL ARG PHE GLU ILE ALA ALA PRO SER HIS ASP GLU TYR SEQRES 13 B 189 SER LEU HIS ILE ASP GLU GLN THR GLY VAL SER GLY ARG SEQRES 14 B 189 PHE TRP SER GLU PRO LEU VAL ALA GLU TRP ASP ASP PHE SEQRES 15 B 189 GLU TRP LYS GLY PRO GLN TRP HET ZN A 302 1 HET SO4 A 501 5 HET CL A 303 1 HET CL A 304 1 HET CL A 306 1 HET EDO A 401 4 HET EDO A 402 4 HET ZN B 301 1 HET SO4 B 502 5 HET CL B 305 1 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 SO4 2(O4 S 2-) FORMUL 5 CL 4(CL 1-) FORMUL 8 EDO 2(C2 H6 O2) FORMUL 13 HOH *175(H2 O) HELIX 1 1 GLU A 79 GLY A 85 5 7 HELIX 2 2 GLU B 79 GLY B 85 5 7 SHEET 1 A 3 PHE A 31 PRO A 32 0 SHEET 2 A 3 LEU A 42 PHE A 49 -1 O TYR A 48 N PHE A 31 SHEET 3 A 3 ARG A 37 VAL A 39 -1 N ARG A 37 O VAL A 44 SHEET 1 B 7 PHE A 31 PRO A 32 0 SHEET 2 B 7 LEU A 42 PHE A 49 -1 O TYR A 48 N PHE A 31 SHEET 3 B 7 CYS A 69 ALA A 77 -1 O HIS A 76 N HIS A 43 SHEET 4 B 7 GLY A 122 VAL A 129 -1 O TYR A 125 N ALA A 73 SHEET 5 B 7 ALA A 115 ALA A 119 -1 N ALA A 115 O GLY A 126 SHEET 6 B 7 SER B 153 HIS B 155 1 O HIS B 155 N ASN A 118 SHEET 7 B 7 MET A 54 HIS A 55 -1 N HIS A 55 O LEU B 154 SHEET 1 C 4 GLN A 110 MET A 113 0 SHEET 2 C 4 ARG A 96 LYS A 103 -1 N ALA A 99 O VAL A 112 SHEET 3 C 4 GLY A 136 ALA A 145 -1 O ALA A 145 N ARG A 96 SHEET 4 C 4 LEU A 171 TRP A 180 -1 O ALA A 173 N PHE A 142 SHEET 1 D 3 PHE B 31 PRO B 32 0 SHEET 2 D 3 LEU B 42 PHE B 49 -1 O TYR B 48 N PHE B 31 SHEET 3 D 3 ARG B 37 VAL B 39 -1 N ARG B 37 O VAL B 44 SHEET 1 E 7 PHE B 31 PRO B 32 0 SHEET 2 E 7 LEU B 42 PHE B 49 -1 O TYR B 48 N PHE B 31 SHEET 3 E 7 CYS B 69 ALA B 77 -1 O HIS B 76 N HIS B 43 SHEET 4 E 7 GLY B 122 VAL B 129 -1 O TYR B 125 N ALA B 73 SHEET 5 E 7 ALA B 115 ALA B 119 -1 N ALA B 115 O GLY B 126 SHEET 6 E 7 SER A 153 HIS A 155 1 N HIS A 155 O ASN B 118 SHEET 7 E 7 MET B 54 HIS B 55 -1 O HIS B 55 N LEU A 154 SHEET 1 F 4 GLN B 110 MET B 113 0 SHEET 2 F 4 ARG B 96 LYS B 103 -1 N ALA B 99 O VAL B 112 SHEET 3 F 4 GLY B 136 ALA B 145 -1 O GLU B 143 N VAL B 98 SHEET 4 F 4 LEU B 171 TRP B 180 -1 O TRP B 175 N VAL B 140 LINK NE2 HIS A 70 ZN ZN A 302 1555 1555 2.20 LINK SD MET A 117 ZN ZN A 302 1555 1555 2.83 LINK NE2BHIS A 124 ZN ZN A 302 1555 1555 1.96 LINK NE2 HIS A 155 ZN ZN B 301 1555 1555 2.33 LINK ZN ZN A 302 NE2 HIS B 155 1555 1555 2.23 LINK NE2 HIS B 70 ZN ZN B 301 1555 1555 2.19 LINK SD MET B 117 ZN ZN B 301 1555 1555 2.78 LINK NE2BHIS B 124 ZN ZN B 301 1555 1555 1.79 CISPEP 1 HIS A 55 PRO A 56 0 -10.78 CISPEP 2 HIS B 55 PRO B 56 0 -6.44 SITE 1 AC1 5 HIS A 155 HIS B 70 GLU B 72 MET B 117 SITE 2 AC1 5 HIS B 124 SITE 1 AC2 4 HIS A 70 MET A 117 HIS A 124 HIS B 155 SITE 1 AC3 6 ARG A 165 TRP A 167 SER A 168 GLU A 169 SITE 2 AC3 6 HOH A 538 HOH B 511 SITE 1 AC4 7 GLY B 34 GLU B 35 ARG B 37 TRP B 175 SITE 2 AC4 7 HOH B 537 HOH B 557 HOH B 561 SITE 1 AC5 2 SER A 148 HIS A 149 SITE 1 AC6 3 GLN A 102 LYS A 139 HOH A 610 SITE 1 AC7 8 PHE A 31 PRO A 32 TYR A 48 ASP A 68 SITE 2 AC7 8 LYS A 130 LYS A 181 GLN A 184 HOH A 505 SITE 1 AC8 5 ARG A 37 TRP A 175 ASP A 176 HOH A 511 SITE 2 AC8 5 HOH A 604 CRYST1 34.071 65.881 150.605 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029350 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006640 0.00000