HEADER METAL TRANSPORT 11-JUL-17 5WFA OBSLTE 29-NOV-17 5WFA 6B2Y TITLE APO YIUA CRYSTAL FORM 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE-BINDING PERIPLASMIC PROTEIN OF IRON/SIDEROPHORE ABC COMPND 3 TRANSPORTER; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 GENE: YIUA, Y2875; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSITION METAL HOMEOSTASIS, YERSINIA PESTIS, CLUSTER A-2, KEYWDS 2 SUBSTRATE-BINDING PROTEIN, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.D.RADKA,L.J.DELUCAS,S.G.ALLER REVDAT 2 29-NOV-17 5WFA 1 OBSLTE REVDAT 1 22-NOV-17 5WFA 0 JRNL AUTH C.D.RADKA,D.CHEN,L.J.DELUCAS,S.G.ALLER JRNL TITL THE CRYSTAL STRUCTURE OF THE YERSINIA PESTIS IRON CHAPERONE JRNL TITL 2 YIUA REVEALS A BASIC TRIAD BINDING MOTIF FOR THE CHELATED JRNL TITL 3 METAL. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 921 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 29095164 JRNL DOI 10.1107/S2059798317015236 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 66955 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 45.5492 - 5.1410 0.98 4787 149 0.1550 0.1658 REMARK 3 2 5.1410 - 4.0814 0.99 4831 149 0.1347 0.1609 REMARK 3 3 4.0814 - 3.5657 0.97 4685 147 0.1523 0.1850 REMARK 3 4 3.5657 - 3.2398 0.98 4828 148 0.1701 0.2243 REMARK 3 5 3.2398 - 3.0076 0.97 4744 149 0.1823 0.2320 REMARK 3 6 3.0076 - 2.8303 0.97 4684 140 0.1820 0.2142 REMARK 3 7 2.8303 - 2.6886 0.97 4717 147 0.1913 0.2047 REMARK 3 8 2.6886 - 2.5716 0.96 4676 145 0.1897 0.1957 REMARK 3 9 2.5716 - 2.4726 0.96 4693 146 0.1967 0.2171 REMARK 3 10 2.4726 - 2.3873 0.96 4713 143 0.1924 0.2315 REMARK 3 11 2.3873 - 2.3126 0.95 4610 144 0.1948 0.2492 REMARK 3 12 2.3126 - 2.2465 0.95 4623 143 0.2000 0.2402 REMARK 3 13 2.2465 - 2.1874 0.96 4634 144 0.1962 0.2381 REMARK 3 14 2.1874 - 2.1340 0.95 4723 144 0.1958 0.2229 REMARK 3 15 2.1340 - 2.0855 0.96 4659 142 0.1958 0.2252 REMARK 3 16 2.0855 - 2.0411 0.96 4665 144 0.2049 0.2172 REMARK 3 17 2.0411 - 2.0003 0.95 4631 144 0.2013 0.2245 REMARK 3 18 2.0003 - 1.9626 0.95 4662 141 0.1927 0.2145 REMARK 3 19 1.9626 - 1.9275 0.95 4577 138 0.1976 0.2350 REMARK 3 20 1.9275 - 1.8948 0.95 4706 145 0.2026 0.2138 REMARK 3 21 1.8948 - 1.8643 0.95 4614 140 0.2059 0.2602 REMARK 3 22 1.8643 - 1.8356 0.94 4587 141 0.2108 0.2467 REMARK 3 23 1.8356 - 1.8086 0.94 4582 144 0.2217 0.2694 REMARK 3 24 1.8086 - 1.7831 0.91 4391 134 0.2259 0.2607 REMARK 3 25 1.7831 - 1.7590 0.90 4421 139 0.2402 0.3025 REMARK 3 26 1.7590 - 1.7362 0.87 4265 128 0.2693 0.3038 REMARK 3 27 1.7362 - 1.7145 0.73 3495 107 0.2927 0.3649 REMARK 3 28 1.7145 - 1.6938 0.56 2737 84 0.3005 0.3686 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.630 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 : 0.007 5310 REMARK 3 ANGLE : 0.889 7208 REMARK 3 CHIRALITY : 0.056 806 REMARK 3 PLANARITY : 0.005 938 REMARK 3 DIHEDRAL : 4.395 3200 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5WFA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000228657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2398 REMARK 200 MONOCHROMATOR : SI(111), DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR AND K-B PAIR OF REMARK 200 BIMORPH MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V712 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK V712 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66955 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5UXS REMARK 200 REMARK 200 REMARK: LONG THIN BARS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% W/V PEG 3350, 10 MM MES PH 5.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K 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 48.32950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A -37 REMARK 465 GLY A -36 REMARK 465 THR A -35 REMARK 465 GLY A -34 REMARK 465 LYS A -33 REMARK 465 GLY A -32 REMARK 465 PHE A -31 REMARK 465 GLY A -30 REMARK 465 VAL A -29 REMARK 465 LYS A -28 REMARK 465 CYS A -27 REMARK 465 VAL A -26 REMARK 465 SER A -25 REMARK 465 LEU A -24 REMARK 465 LYS A -23 REMARK 465 MET A -22 REMARK 465 ALA A -21 REMARK 465 LYS A -20 REMARK 465 GLY A -19 REMARK 465 LEU A -18 REMARK 465 THR A -17 REMARK 465 ILE A -16 REMARK 465 SER A -15 REMARK 465 LEU A -14 REMARK 465 LEU A -13 REMARK 465 PHE A -12 REMARK 465 GLY A -11 REMARK 465 TRP A -10 REMARK 465 ALA A -9 REMARK 465 LEU A -8 REMARK 465 MET A -7 REMARK 465 ALA A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 SER A -3 REMARK 465 ALA A -2 REMARK 465 LEU A -1 REMARK 465 ALA A 0 REMARK 465 HIS A 102 REMARK 465 GLY A 103 REMARK 465 PRO A 104 REMARK 465 GLY A 105 REMARK 465 LYS A 106 REMARK 465 GLY A 107 REMARK 465 LYS A 347 REMARK 465 ARG A 348 REMARK 465 GLU A 349 REMARK 465 LEU A 350 REMARK 465 ASP A 351 REMARK 465 MET B -37 REMARK 465 GLY B -36 REMARK 465 THR B -35 REMARK 465 GLY B -34 REMARK 465 LYS B -33 REMARK 465 GLY B -32 REMARK 465 PHE B -31 REMARK 465 GLY B -30 REMARK 465 VAL B -29 REMARK 465 LYS B -28 REMARK 465 CYS B -27 REMARK 465 VAL B -26 REMARK 465 SER B -25 REMARK 465 LEU B -24 REMARK 465 LYS B -23 REMARK 465 MET B -22 REMARK 465 ALA B -21 REMARK 465 LYS B -20 REMARK 465 GLY B -19 REMARK 465 LEU B -18 REMARK 465 THR B -17 REMARK 465 ILE B -16 REMARK 465 SER B -15 REMARK 465 LEU B -14 REMARK 465 LEU B -13 REMARK 465 PHE B -12 REMARK 465 GLY B -11 REMARK 465 TRP B -10 REMARK 465 ALA B -9 REMARK 465 LEU B -8 REMARK 465 MET B -7 REMARK 465 ALA B -6 REMARK 465 GLY B -5 REMARK 465 SER B -4 REMARK 465 SER B -3 REMARK 465 ALA B -2 REMARK 465 LEU B -1 REMARK 465 ALA B 0 REMARK 465 GLY B 75 REMARK 465 ASN B 76 REMARK 465 THR B 77 REMARK 465 THR B 78 REMARK 465 ALA B 79 REMARK 465 GLY B 101 REMARK 465 HIS B 102 REMARK 465 GLY B 103 REMARK 465 PRO B 104 REMARK 465 GLY B 105 REMARK 465 LYS B 106 REMARK 465 GLY B 107 REMARK 465 SER B 108 REMARK 465 ARG B 348 REMARK 465 GLU B 349 REMARK 465 LEU B 350 REMARK 465 ASP B 351 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 A 809 O HOH A 834 1.59 REMARK 500 O HOH A 521 O HOH A 801 1.60 REMARK 500 O HOH B 501 O HOH B 709 1.62 REMARK 500 O HOH B 689 O HOH B 826 1.67 REMARK 500 O GLN A 265 O HOH A 501 1.73 REMARK 500 O HOH A 526 O HOH A 714 1.80 REMARK 500 O HOH A 544 O HOH A 776 1.81 REMARK 500 OE1 GLN B 70 O HOH B 501 1.93 REMARK 500 O ASN B 128 O HOH B 502 1.95 REMARK 500 N GLN A 269 O HOH A 501 1.95 REMARK 500 OD1 ASN B 200 O HOH B 503 1.95 REMARK 500 O HOH A 637 O HOH A 716 1.96 REMARK 500 O HOH A 691 O HOH A 798 1.98 REMARK 500 O HOH A 504 O HOH A 805 2.00 REMARK 500 O HOH A 620 O HOH A 703 2.02 REMARK 500 O HOH B 561 O HOH B 789 2.07 REMARK 500 O HOH B 736 O HOH B 772 2.08 REMARK 500 O HOH B 711 O HOH B 757 2.08 REMARK 500 NZ LYS A 275 O HOH A 502 2.09 REMARK 500 OD1 ASP A 160 O HOH A 503 2.12 REMARK 500 O PRO A 246 O HOH A 504 2.13 REMARK 500 O CYS A 192 O HOH A 505 2.14 REMARK 500 O HOH A 518 O HOH A 685 2.15 REMARK 500 O HOH B 794 O HOH B 802 2.15 REMARK 500 O HOH A 817 O HOH A 855 2.16 REMARK 500 O ILE B 74 O HOH B 504 2.16 REMARK 500 O HOH A 761 O HOH A 827 2.16 REMARK 500 O HOH A 662 O HOH A 699 2.17 REMARK 500 O HOH A 577 O HOH A 758 2.17 REMARK 500 NH1 ARG B 19 O HOH B 505 2.18 REMARK 500 OE1 GLU A 109 O HOH A 506 2.18 REMARK 500 O VAL A 87 O HOH A 507 2.19 REMARK 500 O HOH B 549 O HOH B 561 2.19 REMARK 500 O THR A 78 O HOH A 508 2.19 REMARK 500 O HOH B 548 O HOH B 572 2.19 REMARK 500 NE ARG B 19 O ASN B 91 2.19 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 O HOH B 806 O HOH B 848 1655 2.03 REMARK 500 O HOH A 873 O HOH A 876 1455 2.04 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 GLU B 109 CD GLU B 109 OE1 0.072 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 A 76 85.19 42.81 REMARK 500 THR A 77 -7.39 -163.84 REMARK 500 SER A 81 -16.36 63.95 REMARK 500 ILE A 82 94.38 53.63 REMARK 500 GLU A 85 -62.78 -103.79 REMARK 500 LYS A 86 -89.97 -94.36 REMARK 500 CYS A 193 48.44 78.75 REMARK 500 ASN A 200 -135.08 39.60 REMARK 500 ASP A 249 -35.25 71.23 REMARK 500 ASN A 297 59.38 -154.90 REMARK 500 SER B 81 -111.91 49.26 REMARK 500 CYS B 193 30.05 76.04 REMARK 500 ASN B 200 -140.21 60.64 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 A 79 ASP A 80 137.32 REMARK 500 CYS A 192 CYS A 193 150.00 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 A 875 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 876 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 877 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH B 868 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH B 869 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH B 870 DISTANCE = 7.36 ANGSTROMS 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 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 61 OH REMARK 620 2 TYR A 300 OH 110.6 REMARK 620 3 HOH A 581 O 117.0 110.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR B 61 OH REMARK 620 2 TYR B 300 OH 114.1 REMARK 620 3 HOH B 539 O 117.9 115.3 REMARK 620 N 1 2 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 HOH A 543 O REMARK 620 2 HOH A 843 O 118.0 REMARK 620 3 HOH B 766 O 78.3 138.0 REMARK 620 4 HOH A 774 O 116.2 95.2 112.3 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 NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WF8 RELATED DB: PDB REMARK 900 5WF8 CONTAINS SAME PROTEIN BUT DIFFERENT CRYSTAL FORM DBREF 5WFA A -37 351 UNP Q8D027 Q8D027_YERPE 1 389 DBREF 5WFA B -37 351 UNP Q8D027 Q8D027_YERPE 1 389 SEQRES 1 A 389 MET GLY THR GLY LYS GLY PHE GLY VAL LYS CYS VAL SER SEQRES 2 A 389 LEU LYS MET ALA LYS GLY LEU THR ILE SER LEU LEU PHE SEQRES 3 A 389 GLY TRP ALA LEU MET ALA GLY SER SER ALA LEU ALA ALA SEQRES 4 A 389 THR VAL THR ASP MET ALA GLY ARG THR VAL THR ILE PRO SEQRES 5 A 389 ALA LYS VAL GLU ARG ILE LEU LEU GLY GLU GLY ARG LEU SEQRES 6 A 389 PHE TYR ALA VAL SER LEU LEU GLU GLY ASN LYS PRO LEU SEQRES 7 A 389 ASP ARG ILE VAL GLY TRP GLN GLY ASP PHE ARG LYS LEU SEQRES 8 A 389 ASP PRO GLN THR TYR ALA ILE TYR LYS ALA LYS PHE PRO SEQRES 9 A 389 GLN ILE ASP GLN ILE PRO LEU ILE GLY ASN THR THR ALA SEQRES 10 A 389 ASP SER ILE SER PRO GLU LYS VAL LEU THR LEU ASN PRO SEQRES 11 A 389 ASP ILE ALA ILE PHE GLY LEU SER GLY HIS GLY PRO GLY SEQRES 12 A 389 LYS GLY SER GLU LEU VAL LYS GLN LEU GLU LYS ALA GLY SEQRES 13 A 389 VAL PRO VAL VAL PHE VAL ASP PHE ARG ASN SER PRO LEU SEQRES 14 A 389 LYS ASN THR LEU PRO SER MET ARG LEU LEU GLY LYS ALA SEQRES 15 A 389 LEU HIS ARG GLU GLN GLN ALA GLU ASN TYR ILE ASN PHE SEQRES 16 A 389 TYR GLN ASP ASN VAL ASP LYS VAL THR ASP ILE THR ASN SEQRES 17 A 389 LYS ILE PRO GLU ASP LYS LYS PRO SER VAL PHE ILE GLU SEQRES 18 A 389 LEU ARG ALA GLY ALA SER GLU GLU CYS CYS GLY THR ALA SEQRES 19 A 389 GLY LYS GLY ASN MET GLY ASP PHE ILE ASP GLN ALA GLY SEQRES 20 A 389 GLY ASN ASN ILE ALA LYS ASN LEU LEU PRO GLY SER LEU SEQRES 21 A 389 GLY THR VAL ASN LEU GLU LYS VAL LEU ALA ALA LYS PRO SEQRES 22 A 389 ASP ILE TYR ILE ALA SER GLY GLY LYS SER PRO GLY SER SEQRES 23 A 389 ASP ALA PRO GLY VAL VAL LEU GLY ALA GLN VAL THR PRO SEQRES 24 A 389 GLU GLN ALA GLN ALA SER LEU GLN LYS ILE LEU GLY ARG SEQRES 25 A 389 LYS GLY ILE ASN THR LEU SER ALA VAL ASN THR GLY HIS SEQRES 26 A 389 SER TYR ALA ILE TRP HIS ASN TYR TYR ASN SER PRO TYR SEQRES 27 A 389 ASN VAL LEU ALA ILE GLN SER PHE ALA LYS TRP PHE TYR SEQRES 28 A 389 PRO GLU GLN PHE ALA ASP LEU ASP PRO LYS LYS THR MET SEQRES 29 A 389 ASP SER LEU TYR SER GLN PHE LEU ALA VAL GLU PRO SER SEQRES 30 A 389 GLY THR TYR TRP ILE GLU ALA LYS ARG GLU LEU ASP SEQRES 1 B 389 MET GLY THR GLY LYS GLY PHE GLY VAL LYS CYS VAL SER SEQRES 2 B 389 LEU LYS MET ALA LYS GLY LEU THR ILE SER LEU LEU PHE SEQRES 3 B 389 GLY TRP ALA LEU MET ALA GLY SER SER ALA LEU ALA ALA SEQRES 4 B 389 THR VAL THR ASP MET ALA GLY ARG THR VAL THR ILE PRO SEQRES 5 B 389 ALA LYS VAL GLU ARG ILE LEU LEU GLY GLU GLY ARG LEU SEQRES 6 B 389 PHE TYR ALA VAL SER LEU LEU GLU GLY ASN LYS PRO LEU SEQRES 7 B 389 ASP ARG ILE VAL GLY TRP GLN GLY ASP PHE ARG LYS LEU SEQRES 8 B 389 ASP PRO GLN THR TYR ALA ILE TYR LYS ALA LYS PHE PRO SEQRES 9 B 389 GLN ILE ASP GLN ILE PRO LEU ILE GLY ASN THR THR ALA SEQRES 10 B 389 ASP SER ILE SER PRO GLU LYS VAL LEU THR LEU ASN PRO SEQRES 11 B 389 ASP ILE ALA ILE PHE GLY LEU SER GLY HIS GLY PRO GLY SEQRES 12 B 389 LYS GLY SER GLU LEU VAL LYS GLN LEU GLU LYS ALA GLY SEQRES 13 B 389 VAL PRO VAL VAL PHE VAL ASP PHE ARG ASN SER PRO LEU SEQRES 14 B 389 LYS ASN THR LEU PRO SER MET ARG LEU LEU GLY LYS ALA SEQRES 15 B 389 LEU HIS ARG GLU GLN GLN ALA GLU ASN TYR ILE ASN PHE SEQRES 16 B 389 TYR GLN ASP ASN VAL ASP LYS VAL THR ASP ILE THR ASN SEQRES 17 B 389 LYS ILE PRO GLU ASP LYS LYS PRO SER VAL PHE ILE GLU SEQRES 18 B 389 LEU ARG ALA GLY ALA SER GLU GLU CYS CYS GLY THR ALA SEQRES 19 B 389 GLY LYS GLY ASN MET GLY ASP PHE ILE ASP GLN ALA GLY SEQRES 20 B 389 GLY ASN ASN ILE ALA LYS ASN LEU LEU PRO GLY SER LEU SEQRES 21 B 389 GLY THR VAL ASN LEU GLU LYS VAL LEU ALA ALA LYS PRO SEQRES 22 B 389 ASP ILE TYR ILE ALA SER GLY GLY LYS SER PRO GLY SER SEQRES 23 B 389 ASP ALA PRO GLY VAL VAL LEU GLY ALA GLN VAL THR PRO SEQRES 24 B 389 GLU GLN ALA GLN ALA SER LEU GLN LYS ILE LEU GLY ARG SEQRES 25 B 389 LYS GLY ILE ASN THR LEU SER ALA VAL ASN THR GLY HIS SEQRES 26 B 389 SER TYR ALA ILE TRP HIS ASN TYR TYR ASN SER PRO TYR SEQRES 27 B 389 ASN VAL LEU ALA ILE GLN SER PHE ALA LYS TRP PHE TYR SEQRES 28 B 389 PRO GLU GLN PHE ALA ASP LEU ASP PRO LYS LYS THR MET SEQRES 29 B 389 ASP SER LEU TYR SER GLN PHE LEU ALA VAL GLU PRO SER SEQRES 30 B 389 GLY THR TYR TRP ILE GLU ALA LYS ARG GLU LEU ASP HET NA A 401 1 HET NA A 402 1 HET NA A 403 1 HET NA B 401 1 HETNAM NA SODIUM ION FORMUL 3 NA 4(NA 1+) FORMUL 7 HOH *747(H2 O) HELIX 1 AA1 GLU A 24 ARG A 26 5 3 HELIX 2 AA2 LEU A 27 LEU A 33 1 7 HELIX 3 AA3 GLY A 48 ASP A 54 1 7 HELIX 4 AA4 ASP A 54 PHE A 65 1 12 HELIX 5 AA5 PRO A 66 ILE A 71 5 6 HELIX 6 AA6 GLU A 109 ALA A 117 1 9 HELIX 7 AA7 SER A 129 LEU A 145 1 17 HELIX 8 AA8 ARG A 147 ASN A 170 1 24 HELIX 9 AA9 LYS A 171 ILE A 172 5 2 HELIX 10 AB1 PRO A 173 LYS A 177 5 5 HELIX 11 AB2 ASN A 200 ALA A 208 1 9 HELIX 12 AB3 ASN A 226 LYS A 234 1 9 HELIX 13 AB4 THR A 260 GLY A 273 1 14 HELIX 14 AB5 GLY A 276 THR A 279 5 4 HELIX 15 AB6 LEU A 280 THR A 285 1 6 HELIX 16 AB7 ASN A 294 TYR A 300 5 7 HELIX 17 AB8 ASN A 301 TYR A 313 1 13 HELIX 18 AB9 ASP A 321 LEU A 334 1 14 HELIX 19 AC1 GLU B 24 ARG B 26 5 3 HELIX 20 AC2 LEU B 27 LEU B 33 1 7 HELIX 21 AC3 GLY B 48 ASP B 54 1 7 HELIX 22 AC4 ASP B 54 PHE B 65 1 12 HELIX 23 AC5 PRO B 66 ILE B 71 5 6 HELIX 24 AC6 GLU B 85 ASN B 91 5 7 HELIX 25 AC7 LEU B 110 LYS B 116 1 7 HELIX 26 AC8 SER B 129 LEU B 145 1 17 HELIX 27 AC9 ARG B 147 ASN B 170 1 24 HELIX 28 AD1 LYS B 171 ILE B 172 5 2 HELIX 29 AD2 PRO B 173 LYS B 177 5 5 HELIX 30 AD3 ASN B 200 ALA B 208 1 9 HELIX 31 AD4 ASN B 226 LYS B 234 1 9 HELIX 32 AD5 THR B 260 GLY B 273 1 14 HELIX 33 AD6 GLY B 276 THR B 279 5 4 HELIX 34 AD7 LEU B 280 THR B 285 1 6 HELIX 35 AD8 ASN B 294 TYR B 300 5 7 HELIX 36 AD9 ASN B 301 TYR B 313 1 13 HELIX 37 AE1 ASP B 321 LEU B 334 1 14 SHEET 1 AA1 2 THR A 2 THR A 4 0 SHEET 2 AA1 2 THR A 10 THR A 12 -1 O VAL A 11 N VAL A 3 SHEET 1 AA2 5 LEU A 73 ILE A 74 0 SHEET 2 AA2 5 ILE A 43 GLN A 47 1 N TRP A 46 O ILE A 74 SHEET 3 AA2 5 ILE A 20 LEU A 22 1 N LEU A 22 O GLN A 47 SHEET 4 AA2 5 ILE A 94 GLY A 98 1 O ILE A 96 N LEU A 21 SHEET 5 AA2 5 VAL A 121 VAL A 124 1 O VAL A 122 N ALA A 95 SHEET 1 AA3 5 ASN A 211 ASN A 212 0 SHEET 2 AA3 5 SER A 179 GLU A 183 1 N VAL A 180 O ASN A 211 SHEET 3 AA3 5 ILE A 237 GLY A 242 1 O ILE A 239 N GLU A 183 SHEET 4 AA3 5 SER A 288 TRP A 292 1 O ILE A 291 N ALA A 240 SHEET 5 AA3 5 TRP A 343 GLU A 345 -1 O ILE A 344 N ALA A 290 SHEET 1 AA4 2 GLY A 194 ALA A 196 0 SHEET 2 AA4 2 LEU A 222 THR A 224 -1 O GLY A 223 N THR A 195 SHEET 1 AA5 2 THR B 2 THR B 4 0 SHEET 2 AA5 2 THR B 10 THR B 12 -1 O VAL B 11 N VAL B 3 SHEET 1 AA6 5 LEU B 73 ILE B 74 0 SHEET 2 AA6 5 ILE B 43 GLN B 47 1 N TRP B 46 O ILE B 74 SHEET 3 AA6 5 ILE B 20 LEU B 22 1 N ILE B 20 O VAL B 44 SHEET 4 AA6 5 ILE B 94 GLY B 98 1 O ILE B 96 N LEU B 21 SHEET 5 AA6 5 VAL B 121 VAL B 124 1 O VAL B 122 N ALA B 95 SHEET 1 AA7 5 ASN B 211 ASN B 212 0 SHEET 2 AA7 5 SER B 179 GLU B 183 1 N VAL B 180 O ASN B 211 SHEET 3 AA7 5 ILE B 237 GLY B 242 1 O ILE B 239 N GLU B 183 SHEET 4 AA7 5 SER B 288 TRP B 292 1 O TYR B 289 N ALA B 240 SHEET 5 AA7 5 TRP B 343 GLU B 345 -1 O ILE B 344 N ALA B 290 SHEET 1 AA8 2 GLY B 194 ALA B 196 0 SHEET 2 AA8 2 LEU B 222 THR B 224 -1 O GLY B 223 N THR B 195 SSBOND 1 CYS A 192 CYS A 193 1555 1555 2.05 LINK OH TYR A 61 NA NA A 402 1555 1555 2.51 LINK OH TYR A 300 NA NA A 402 1555 1555 3.00 LINK OH TYR B 61 NA NA B 401 1555 1555 2.65 LINK OH TYR B 300 NA NA B 401 1555 1555 2.78 LINK NA NA A 402 O HOH A 581 1555 1555 2.93 LINK NA NA A 403 O HOH A 543 1555 1555 2.23 LINK NA NA A 403 O HOH A 843 1555 1555 2.41 LINK NA NA A 403 O HOH B 766 1555 1555 2.64 LINK NA NA A 403 O HOH A 774 1555 1555 2.51 LINK NA NA B 401 O HOH B 539 1555 1555 2.69 SITE 1 AC1 3 TYR A 61 TYR A 300 HOH A 581 SITE 1 AC2 5 ASP A 206 HOH A 543 HOH A 774 HOH A 843 SITE 2 AC2 5 HOH B 766 SITE 1 AC3 3 TYR B 61 TYR B 300 HOH B 539 CRYST1 46.334 96.659 74.191 90.00 100.67 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 0.021582 0.000000 0.004067 0.00000 SCALE2 0.000000 0.010346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013716 0.00000